University of Illinois
Institute of Natural Resource Sustainability
William Shilts, Executive Director
ILLINOIS NATURAL HISTORY SURVEY
Brian D. Anderson, Director
1816 South Oak Street
Champaign, IL 61820
217-333-6830
Developing a Multimetric Habitat Index for
Wadeable Streams in Illinois
Laura Sass1, Leon C. Hinz Jr.1, John Epifanio1,
and Ann Marie Holtrop2
1
Illinois Natural History Survey
Institute of Natural Resource Sustainability
University of Illinois Champaign-Urbana
2
Illinois Department of Natural Resources
Watershed Protection Section
Prepared for: Illinois Natural History Survey
Project Name:
Developing a Multimetric Habitat Index for Wadeable Streams in Illinois
Grant / Project Number: (T-25-P-001)
INHS Technical Report 2010 (21)
Date of issue: 24 June 2010
Illinois Natural History Survey
Institute of Natural Resource Sustainability
(May 1, 2006 - December 31, 2009)
Developing a Multimetric Habitat Index for
Wadeable Streams in Illinois
Final Project Report 2010
Laura Sass, Leon C. Hinz Jr., John Epifanio, and Ann Marie Holtrop
Submitted to
Illinois Department of Natural Resources
One Natural Resources Way
Springfield, Illinois 62702-1271
24 June 2010
Illinois Natural History Survey Technical Report 2010/21
Developing a Multimetric Habitat Index for
Wadeable Streams in Illinois
Final Project Report
Project: T-25-P-001
(May 1, 2006 - December 31, 2009)
Laura Sass, Leon C. Hinz Jr., John Epifanio, and Ann Marie Holtrop
Illinois Natural History Survey
Institute of Natural Resource Sustainability
1816 South Oak Street
Champaign, Illinois 61820
24 June 2010
__________________________
Dr. John Epifanio,
Project Coordinator
Illinois Natural History Survey
__________________________
Dr. Brian Anderson,
Chief
Illinois Natural History Survey
ACKNOWLEDGMENTS
We would like to acknowledge all of the people who have helped us with their valuable time and
input for this project including the IDNR streams biologists, IEPA, and the summer field
technicians. Special thanks to Roy Smogor, Brian Metzke, and Leslie Bol. Also to Dr. Robert
(Bud) Fischer and his students at Eastern Illinois University who assisted with protocol
development and field collections of habitat data. Funding was provided to the Illinois Natural
History Survey through Illinois’ State Wildlife Grant Program (T-25-P-001).
iii
Developing a Multimetric Habitat Index for Wadeable Streams in Illinois
Acknowledgements ........................................................................................................................ iii
Table of Contents ........................................................................................................................... iv
List of Tables .................................................................................................................................. v
List of Figures ................................................................................................................................ vi
List of Appendices ........................................................................................................................ vii
Introduction ..................................................................................................................................... 1
JOB 1. Rate sites for disturbance. ................................................................................................... 2
1.1 Investigate utility of using existing disturbance ratings developed by Smogor (2000). ...... 2
1.3 Select sites with range of disturbance for sampling............................................................. 5
JOB 2. Identify potential metrics. .................................................................................................. 6
2.2 Develop sampling techniques for each candidate metric. .................................................... 6
2.3 Sample metrics at chosen sample sites. ............................................................................... 9
JOB 3. Determine regions ............................................................................................................... 9
3.1 Identify possible regionalization schemes (e.g., watersheds, natural divisions). ................ 9
3.2 Identify degree to which metrics sample at least-disturbed sites differ among regions. ... 10
3.3 Select final regions. ............................................................................................................ 11
JOB 4. Select final metrics........................................................................................................... 11
JOB 5. Develop scoring criteria for each region.......................................................................... 12
5.1 Establish regional scoring criteria for each metric. ........................................................... 12
JOB 6. Prepare final report. ......................................................................................................... 13
6.1 Prepare final report including a “how to” manual. ............................................................ 13
6.2 Conduct a training workshop. ............................................................................................ 13
Literature Cited ............................................................................................................................. 14
iv
List of Tables
Table 1. Land cover classes used for delineation of land cover types for analyses of
disturbance in whole and local watersheds and local riparian zones (Luman and Joselyn
1996). ................................................................................................................................ 17
Table 2. Total number of sites sampled by IBI region and disturbance class. ................ 18
Table 3. Metrics and scores comprising Illinois’ Stream Habitat Assessment Procedure
(SHAP). The overall index value is determined as the sum of individual metric scores and
ranges from 5 – 24. Higher values indicate site conditions more similar to those of least
disturbed sites within their region. .................................................................................... 19
Table 4. Metric comprising Ohio’s Qualitative Habitat Evaluation Index (QHEI; gradient
omitted). ............................................................................................................................ 20
Table 5. Candidate metrics that were collected by field staff for metric development
(Appendix B). Scale refers to whether the metric was recorded for each individual
channel unit (e.g., run, riffle, pool, or transitional), for the entire sampling reach, or both.
........................................................................................................................................... 22
Table 6. Substrate and bottom type categories used in stream habitat assessment taken
from Illinois’ Stream Habitat Assessment Procedure (SHAP; IEPA 1994). .................... 23
Table 7. Buffer categories used in stream habitat assessment. ........................................ 24
Table 8. Cover definitions for channel units. Amount of each cover type is estimated as
none, sparse, intermediate or abundant. ............................................................................ 25
Table 9. Stream classes were determined by gradient and size. Gradient was measured
as percent slope. Stream size was measured by link number. Table 9a provides the
ranges for size and gradient with in each class. Every stream arc was given two numbers;
one for the corresponding gradient group and one for size. These number were combined
categorically (e.g., a stream a with link number 25 and a gradient of 0.0012 would be put
in the 21 category for stream class). Table 9b provides the number of sites sampled in
each disturbance class for each stream type. .................................................................... 26
Table 10. Model significance results reported for the Multivariate Analysis of Variance
(MANOVA) run on candidate regionalization schemes using potential index metrics.
Numbers with a box around them and highlighted yellow (grey) indicate a significance
level of p≤0.05. Dependent variables are defined in Appendix A. .................................. 27
Table 11. Number of sites sampled in each disturbance class in each ecoregion. ........... 28
Table 12. List of the final candidate metrics narrowed down from the original 200. The
final five metrics used are listed first. ............................................................................... 29
v
List of Figures
Figure 1. Sketch of a local watershed, total upstream catchment, and riparian zone.
Local watersheds pertain to area draining directly to the specific stream arc, while the
catchments include all upstream drainage area. Riparian zone included a 150 m buffer
centered on the stream arc. The riparian zone did not extend up into the total catchment.
........................................................................................................................................... 30
Figure 2. Distribution map of disturbance ratings for proportions of disturbed land in the
whole watersheds of Illinois streams. Stream arcs are color coded by disturbance rating:
1-5 = blue, 6-10 = green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate
less disturbance of this type. ............................................................................................. 31
Figure 3. Distribution map of disturbance ratings for the volume of impounded water in
the whole watershed of each stream arc. Stream arcs are color coded by disturbance
rating: 1 = grey, 2-5 = blue, 6-10 = green, 11-15 = yellow, 16-20 = red. Smaller numbers
ratings indicate less disturbance of this type..................................................................... 32
Figure 4. A map showing an example of the proportion of strip-mined land (gray) in
each watershed assessed (black outlines in the inset). Proportions were calculated by
dividing the area of each watershed in strip-mined land by the total area of that
watershed. Proportions were used to determine disturbance classes for each disturbance
type (Figure 5)................................................................................................................... 33
Figure 5. Distribution map of disturbance ratings for strip-mined land affecting Illinois
streams. Stream arcs are color coded by disturbance rating: 1 = grey, 2-5 = blue, 6-10 =
green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate less disturbance of
this type. ............................................................................................................................ 34
Figure 6. Distribution map of disturbance ratings for undisturbed land uses in the
riparian zones of Illinois streams. Stream arcs are color coded by disturbance rating: 1-5
= blue, 6-10 = green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate
less disturbance of this type. ............................................................................................. 35
Figure 7. Distribution map of disturbance ratings for the density of road crossing in the
local watershed for Illinois streams. Stream arcs are color coded by disturbance rating: 15 = blue, 6-10 = green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate
less disturbance of this type. ............................................................................................. 36
Figure 8. Map depicting total disturbance classes for stream arcs in Illinois. Blue
streams are least disturbed (lower 15th percentile), green are moderately disturbed and red
streams are most disturbed (upper 90th percentile). .......................................................... 37
vi
Figure 9. Map of Illinois showing the location of all sampled sites. Blue circles
represent sample locations on streams that are least disturbed, green are moderately
disturbed and red circles are sample locations on most disturbed stream arcs. ................ 38
Figure 10. Maps delineating the regionalization schemes considered to address regional
variation in habitat measures: a. Fish IBI regions, b. Freshwater ecoregions, c.
Ecoregions of Illinois, d. Glacial boundaries, e. Natural Divisions, and f. major
watersheds. ........................................................................................................................ 39
Figure 11. Map of Illinois delineated by ecoregions (Woods et al. 2006) and showing the
location of all sampled sites. Blue circles represent sample locations on streams that are
least disturbed, green are moderately disturbed and red circles are sample locations on
most disturbed stream arcs. ............................................................................................... 40
Figure 12. Proportion of large woody debris (p_LWD) by disturbance class. ................ 41
Figure 13. Range of index scores for each disturbance class. A lower index score
indicates a less disturbed stream. Index scores range from 5-24. .................................... 42
List of Appendices
Appendix A. A list of all candidate metrics examined. ................................................... 43
Appendix B. Example field sheets including information collected at each site. ............ 53
Appendix C. Statewide and Regional Scoring Plots for the Illinois Habitat Index. ......... 55
Appendix D. Procedure for Physical Habitat Measurements and Scoring of the Illinois
Habitat Index. .................................................................................................................... 70
vii
Developing a multimetric habitat index for wadeable streams in Illinois
Introduction
In Illinois, several methods are used to collect and summarize habitat information in
wadeable streams. Methods range from relatively rapid, subjective, visually-based
surveys used by Illinois Department of Natural Resources (IDNR), to quantitative pointtransect surveys used by Illinois Environmental Protection Agency (IEPA) and the
Illinois Natural History Survey (INHS). The intensity of point-transect methods vary, but
biologists often spend 1.5-2 hours per site collecting habitat data. Although these data
provide a detailed description of stream conditions when sampling occurred, some
features (e.g., wetted width) vary in response to seasonal conditions and weather events.
Therefore, detecting meaningful changes in stream quality is difficult.
Another approach used by the IEPA is to use data collected through point-transect
methods to measure biological potential, or the ability of a stream to support a healthy
aquatic community where chemical and non-chemical stressors are not present (Barbour
et al. 1997). Consequently, Hite and Bertrand (1989) developed the Predicted Index of
Biotic Integrity (PIBI) by using multiple regression analysis that identified the stream
habitat metrics most strongly related to biotic integrity as measured by the fish-based
Index of Biotic Integrity (IBI; Karr et al. 1986). Although predicting the biotic potential
of a stream is useful for determining causes of impairment (e.g., lack of habitat) and
identifying sites with restoration potential, it does not facilitate comparisons among
streams.
Frequently, qualitative habitat indices are used to rate a stream’s physical environment
(Stauffer and Goldstein 1997). These indices are less subjective than visually-based
surveys and require less time and staff than point-transect methods. A measure employed
in Illinois to ascertain stream habitat quality is the Stream Habitat Assessment Procedure
(SHAP; IEPA 1994), a qualitative index comprised of 15 metrics. Illinois EPA
developed SHAP to facilitate comparisons of stream quality across sites. To develop the
index, qualitative habitat metrics were regressed against total IBI scores and individual
IBI metrics and were ranked by R-square values (IEPA unpublished data, Marion office).
Metrics that were highly correlated with IBI scores were selected for SHAP, and were
subsequently assigned a scoring range that corresponded to their relative importance to
fish communities. Although SHAP is a useful tool for comparing stream quality across
sites, the metric scores are somewhat subjective and lack adjustment for natural
variability throughout Illinois. Moreover, the metrics comprising SHAP may not provide
clear signals of how streams respond to land use impacts on watersheds and streams.
1
Currently in Illinois, the Qualitative Habitat Evaluation Index (QHEI) is used to measure
habitat features that generally correspond to the physical factors affecting fish
communities and other aquatic life (Rankin 1989). As with SHAP, the QHEI metrics
were selected because of strong correlation with stream fish communities (as measured
by IBI) and not because of their response to human impacts. Although QHEI has less
personal bias associated with scoring each metric, the index is based on a single set of
scoring criteria that are applied statewide. Thus, regional differences that exist under
natural conditions (i.e., conditions that are minimally impacted by humans) are not taken
into consideration.
As Illinois’ Wildlife Action Plan is implemented, there is a need for a habitat index that
reflects improvements and deteriorations in aquatic systems. The main objective of this
project was to develop a multi-metric habitat index for use in wadeable streams that was
rapid to conduct, adjusted for regional differences that exist under natural conditions, and
able to detect meaningful changes in a stream over time.
JOB 1. Rate sites for disturbance.
1.1 Investigate utility of using existing disturbance ratings developed by Smogor
(2000).
Smogor (2000) used watershed measures of disturbance (i.e., proportion of undisturbed,
disturbed, and strip-mined land; volume of impounded water and impounded industrial,
mining and sewage waste water; and density of sewage and hazardous point sources) and
site-specific measure of disturbance (e.g., stream-habitat condition, water and sediment
chemistry measures) to rate community fish samples for degree of disturbance. Fish
samples were identified as least, moderately or most disturbed and each potential IBI
metric was examined for meaningful differences among these disturbance classes.
Project staff from the INHS discussed in detail existing disturbance ratings with Ann
Holtrop (IDNR), Dr. Robert Fischer (Eastern Illinois University) and Roy Smogor
(IEPA) and concluded that additional data were available at finer resolutions, which
would allow for a significant improvement over the Smogor (2000) ratings. During the
development of the Fish IBI, Smogor (2000) divided the state into approximately 800
watersheds. All sampling stations located within an individual watershed were assigned
a common disturbance rating regardless of where disturbances were located within the
watershed (e.g., upstream or downstream of the site). Currently, available data have
allowed us to assess disturbance for much smaller watersheds (approximately 57,000
watersheds; Cordle et al. 2006) eliminating potential problems with downstream
disturbances inappropriately being associated with upstream sites. Using some of the
disturbance measures Smogor used to rate fish samples may not affect instream habitat
similarly. Additionally, Smogor (2000) used site-specific measures of disturbance which
were similar to features we planned to measure in this project. Therefore an alternative
approach was developed to address these issues and to prevent circular reasoning.
2
1.2. Develop alternative disturbance rating scheme if needed.
Since human activities at different spatial scales may impact stream habitat we
considered disturbance broadly using several potential measures that function at different
scales. We attempted to parallel the measures used by Smogor (2000) but revised them
to incorporate finer resolution data, eliminate disturbance measures that may not be
applicable to a physical habitat index (e.g., NDPES Permit locations), and add any new
measures that can now be attributed to stream reaches (e.g., density of road crossings).
Each potential measure was summarized at three spatial scales: (1) riparian zone (150 m
buffer), (2) local watershed (area draining directly to the stream arc only, including the
riparian zone), and (3) the total catchment (all upstream area, including the local
watershed; Figure 3). Correlations between potential measures of disturbance
summarized for the local watershed, total catchment and riparian zone were examined to
determine if differences in scale were evident for each measure at individual stream
reaches. The scale used for each disturbance measure was determined based on the level
of the expected effect (e.g., road crossings would have local effects) and to minimize
redundancy in use of the measures (e.g., disturbed land and undisturbed land are
measured at different scales). Following our review, we selected five measures to
include in the disturbance rating: (1) proportion of disturbed land in the total catchment,
(2) maximum volume of impounded water in the total catchment, (3) proportion of stripmined land in the local watershed, (4) proportion of undisturbed land in the riparian
buffer, and (5) density of road crossings in the local watershed. A description of each
selected disturbance measure and how it was scored follows.
1.2.a. Identify alternative measures of disturbance
Proportion of disturbed land
Disturbances from land use practices have been implicated as the cause of excessive
stream habitat degradation including, but not limited to soil erosion and sedimentation
(Roth et al. 1996). Other studies as well have indicated that measurement of land use
disturbances is most appropriate at the catchment scale due to potential downstream
impacts that poor land use practices may have on stream habitat (Allan et al. 1997,
Lammert and Allan 1999, Roth et al. 1996). We chose to account for these processes
using disturbed land in the total catchment. Proportion of disturbed land in the total
catchment was calculated using land cover data from the Critical Trends Assessment
Land Cover Database of Illinois (Luman and Joselyn 1996). Each stream arc (i.e.,
confluence to confluence section) statewide has been attributed with land cover type in
the riparian zone, local watershed, and total catchment as part of a previous project
(Cordle et al. 2006; Figure 1). Disturbed land uses (i.e., agricultural, urban and barren
land delineations (cover types: agricultural = types 8, 9, 10; urban = types 1, 3, 4, 11;
barren = type 23; Table 1) for the total catchment. Since these data were relatively
normally distributed, the data were standardized into 20 equal scores (range 1-20; Figure
2).
3
Maximum volume of impounded water
Damming the natural flow of a stream not only reduces flow volume of a stream, but can
also starve the water downstream of the impoundment of its natural sediment load. To
restore this loss, the water will erode new materials from the stream banks or stream
substrate. Volume of impounded water was measured within the entire upstream
catchment to provide insight into the magnitude of the impact. Maximum storagevolume of impounded water (industrial, mining, or sewage-waste water) was calculated
from the National Inventory of Dams 1995 and the Illinois Water Survey Dams Database
1997. We summed the volume of water upstream of each stream arc and attributed this
volume to the arc. The volume of impounded water was divided by the area of the entire
upstream catchment for a proportional measurement of impounded water (x 1,000 cubic
m / square km). These data were highly skewed with many sites having no impounded
water and a few sites had very large volumes of impounded water, therefore sites with no
impounded water were assigned a score of 1, and sites with large amounts of water
(upper 90th percentile) were assigned a score of 20. The remaining sites were
standardized into 18 equal scores (range 2-19; Figure 3)
Proportion of strip-mined land
Strip-mining can have negative impacts on stream habitat, particularly associated with
accumulation of fine sediments in runoff from mining sites. Strip-mined land was
measured at the local watershed scale because the direct effects of strip-mining (e.g.,
increased runoff and sedimentation) would be most noticeable near the source.
Proportion of strip-mined land (active post 1949) in the local watershed was determined
using the total area of strip-mined land divided by the local watershed area (Figure 4).
The distribution of proportions was highly skewed toward sites without mining impacts;
therefore sites with zero mining in the local watershed were assigned a score of 1. The
remaining proportions were standardized to 19 equal scores (range 2-20; Figure 5).
Proportion of undisturbed land
Disturbance in the riparian zone has been demonstrated to have systemic effects (e.g.,
changes in the hydrograph) on stream networks that can be observed locally as channel
erosion and decreased bank stability. However, the positive effects of riparian protection
are not likely to extend far beyond the area protected. Undisturbed land in the riparian
buffer best represents the natural landscape associated with local habitat characteristics
and channel development. Intact riparian zones can mitigate some of the systematic
effects of watershed disturbance. Therefore we measured the proportion of undisturbed
land at the riparian scale to account for local improvements in stream habitat associated
with these conditions.
Land cover summaries for undisturbed land were available from previous work (Cordle et
al. 2006) based on Luman and Joselyn (1996). The proportion of undisturbed land in the
riparian zone was calculated using spatial data from the Critical Trends Assessment Land
Cover Database of Illinois (cover types: upland forest = types 13, 14, 15; bottom land
forest = types 20, 21; wetland = types 18, 19; Luman and Joselyn 1996; Table 1). These
data were relatively normally distributed, therefore the data were standardized into 20
equal scores (range 1-20; Figure 6)
4
Density of road crossings
Road crossings influence instream habitat by providing a direct conduit for runoff and
sediment transport and potentially altering the path of the channel. Due to the localized
nature of these impacts, the density of road crossings was measured at the local
watershed scale (Tiemann 2004, Hedrick et al. 2009). Density of road crossings was
calculated by summing road-stream intersections and dividing by local watershed area
(road crossings/km2). The data were skewed with a few watersheds having very high
road crossing density, therefore the upper 90th percentile was given a score of 20 and the
remaining data were standardized into 19 equal scores (range 1-19; Figure 7).
1.2.b. Development of a Total Disturbance Score
The five disturbance-measure scores were summed to yield a total disturbance score for
every stream arc (range 5-100). Total disturbance scores for all stream arcs in the state
were plotted and natural breaks in the data were used to delineate least, moderately and
most disturbed classes. Least disturbed sites comprised the lower 15th percentile range of
the total disturbance scores, and most disturbed sites comprised the upper 90th percentile
(Figure 8). Potential sampling sites were assigned the disturbance class of the stream arc
on which each was located (Figure 9).
1.3. Select sites with range of disturbance for sampling
Sites were not selected to be statistically representative of Illinois streams (i.e., at
random) but were selected to provide an adequate coverage of least, moderately and most
disturbed streams within preliminary regions as well as to provide a statewide coverage
of sample points. The regions chosen for the Fish IBI (Smogor 2000) were used to
stratify the state to provide adequate coverage for other possible regionalization schemes.
Thirty sites were chosen per IBI region to represent approximately similar gradients of
disturbance within each for a total of 390 sites targeted. Potential sites were initially
given priority if they were part of the IEPA/IDNR basin rotation, if they had fish IBI
scores associated with them, or if other data were available or scheduled to be collected
from that site.
During the months of May–September, each site was visited and assessed for potential to
sample. If a site met the criteria for sampling (i.e., accessible, wadeable, and not
intermittent) it was sampled at that time. If a site did not meet the criteria (i.e., was not
wadeable or was intermittent), a decision was made as to whether or not the site should
be revisited at a later date. If it was decided that the site was simply too small or too
large to sample, it was discarded as a sampling point and was not revisited. Additional
sites were chosen as needed to fill in gaps in the data coverage. Overall, 514 sites were
sampled (Table 2).
5
JOB 2. Identify potential metrics.
2.1. Identify a list of candidate metrics by reviewing existing indices and the
literature.
Potential habitat features were chosen by reviewing primarily SHAP (IEPA 1994; Table
3) and the QHEI (Rankin 1989; Table 4) because these are the qualitative indexes that
have been or are currently being used by state agencies in Illinois. Other features were
added based on discussions with the project team (e.g., use of features identified in Platts
et al. 1983, Schumm 1960; see Appendix A). Because these methods contain metrics that
are aggregates of in-stream habitat measures, we developed sampling protocols that
would allow combining measurements in a variety of ways.
2.2. Develop sampling techniques for each candidate metric.
Sampling techniques were discussed at length with our collaborators from Eastern Illinois
University and procedures were developed to facilitate data collection (Appendix B).
Methods were fine-tuned during the 2006 field season. Habitat features were sampled at
the whole reach and channel unit scales (Table 5). Definitions for substrate type (Table
6) and in-stream cover (Table 7) were based on existing methods (IEPA 1994).
At each stream sample site, a reach was defined as 20 times the mean stream wetted
width with a minimum of 100 m and a maximum of 300 m plus the distance needed to
reach the end of the final channel unit. When the final channel unit had no observable
endpoint (e.g., a straight channelized ditch) the reach was defined as the shorter distance
of 20 times the mean width or 300 m. We began each reach a minimum of 10 m
upstream of an access point (most often a bridge or crossing) in order to minimize any
effects of the access point (i.e., bridge effects). If the upstream side of the access point
was inaccessible, or if state biologists routinely sample downstream of the access point,
then the habitat was also sampled on the downstream side. Sampling was conducted by
walking the length of the reach first to obtain an overall impression of the reach, then
data were collected and a map was drawn of the reach as the samplers walked back to the
access point.
At the reach scale, data were collected to describe the buffer and stream bank quality and
stability, predominant channel unit type, substrate dominance, flow and depth variability,
channel development and modifications, and average wetted width (Table 5; Appendix
B). Predominant channel type for the reach was described as pool, riffle, or run.
Dominance at the reach scale was estimated as the proportion of total reach length and
not the number of channel units of a given type. For example, it was possible to have
only one of five channels units defined as a pool, yet the predominant channel type could
be “pool” if the majority of the reach was encompassed in this pool.
The buffer zone was assessed from the top of stream bank to 100 m away from the stream
channel. The stream bank (i.e., the top of the water to the top of the bank) was assessed
separately and not considered part of the buffer zone. The width of the buffer was
visually estimated for each side of the stream and placed within one of six categories:
none, very narrow, narrow, moderate, wide and very wide (Table 7). Acceptable cover
within a buffer zone included trees, grasses, un-manicured shrubbery, and bare areas (if
6
naturally bare, for example, due to recent flooding or bedrock). Grasses that were
coarsely mowed between a stream and an agricultural field were considered buffer, but
mowed grass as in a manicured lawn was not. Grazed pastures were considered
agriculture and not counted as buffer. Dominant type of vegetation in the buffer was
categorized as trees, woody/shrub, or herbaceous. If the vegetation within the buffer area
did not have a dominant cover, but rather a mix of trees, woody and/or herbaceous
material, “mixed” was marked as the cover type.
Bank cover was categorized separately for left and right stream banks. Categories of
stream bank cover types were assessed as herbaceous vegetation, woody/shrub
vegetation, trees, bare earth, and bedrock. The amount of stream bank covered by each
category was estimated as none, sparse, intermediate or abundant. In addition to
categorizing the types of cover on the stream bank, the amount of stream surface
receiving sunlight between 10:00 am and 4:00 pm was estimated. The degree of shading
was recorded as: water surface completely shaded; water mostly shaded with some
sunlight; half water surface shaded, half full sunlight; most water surface receiving
sunlight; lack of canopy, full sunlight reaching water.
Substrate was estimated at both the reach and channel unit scales. The dominant and
subdominant substrate types for the reach and for each channel unit were visually
estimated and recorded as boulder, slab boulder, cobble, gravel, fine gravel, sand,
hardpan, silt or bedrock (Table 6). We used substrate types and size categories defined in
the IEPA Quality Assurance and Field Methods Manual, Section E (IEPA 1994).
Flow was visually estimated as fast, moderate, slow, or no detectable flow for the entire
reach and within each channel unit. While relative current velocities are somewhat
dependent of stream type (i.e., fast flow in Illinois streams may be considered moderate
flow in a higher gradient stream); these categories capture the general velocity of the
water within the respective streams.
Ten depths were measured throughout each reach at approximately equal intervals.
These depths generally followed the maximum depth within the channel units (i.e.,
thalweg) and essentially followed the bulk of the flow.
The concept of channel evolution was defined by Schumm et al. (1984) as the pattern of
adjustment by a channel in response to human perturbations (e.g., increasing runoff,
channelization, dredging, and mining). Channel evolution was assessed based on the
descriptions of Schumm et al. (1984) as stable, incising, widening, stabilizing or stable
(successional).
Each channel unit was identified as a mid-channel pool, lateral pool, run, riffle or
transitional area. Mid-channel pools were defined as an area within the stream channel
with little to no flow, in these units, sediment accumulation is expected during base flow
and the thalweg is generally in the middle of the wetted width. Lateral pools were
defined as areas with little or no flow and the thalweg distinctively skewed to one side of
the wetted width at normal base flow. Runs are defined as areas with slow to fast flow,
with depths generally deeper than riffles but shallower that pools. Riffles were sampled
7
where the water depth and/or gradient of the stream made the surface of the water break
into ripples. Flow in riffles was most often moderate to fast. Transitional areas were
areas of a reach that were difficult to define due to mixed attributes. For example, an
area that is shallow with little to no flow (therefore not a riffle, but to shallow to be a run
or pool) may be defined as a transitional area because the unit did not definitively fall
into one channel unit category.
Each channel unit was evaluated. Substrate dominance and flow were recorded in each
channel unit as described previously. Maximum depth was recorded for every channel
unit and eight depths were measured along a cross-section of the deepest portion of each
pool.
In-stream cover was estimated within each channel unit (Table 8). Cover was only
assessed if it was at or below the current water level. For example, a root wad was not
included in the amount of cover in this category if it was exposed on the stream bank.
Eight categories of cover were assessed: aquatic macrophytes, undercut bank,
overhanging vegetation, root wads, root mats, boulders, logs or woody debris, aggregate
large woody debris (LWD). Amount of cover in each category was estimated as none,
sparse, intermediate or abundant. Overhanging vegetation was only considered as cover
if it was within 1 m from the water surface. Abundance of individual logs or woody
debris was estimated separately from aggregate LWD because each can function as
different habitat. For example, inputs of small debris and individual logs provides the
food base for macroinvertebrates and other microorganisms while aggregates of logs can
provide cover and protection from flow for fishes and invertebrates. For any other cover
found, the amount was assessed as “other” and the type was written down.
Embeddedness is a measure of how constrained larger substrates are by smaller particles;
therefore it was not assessed for channel units in which substrate smaller than fine gravel
was dominant. Embeddedness was recorded as: not embedded, 0-25%, 25-50%, 50-75%
or 75-100% embedded. Because deposition is expected in pools at low flows,
embeddedness was not assessed in mid-channel or lateral pools.
The depth of fines (i.e., sand, silt or clay) was measured within each channel unit where
fines were not the dominate substrate type to account for unexpected deposition of
sediment in the reach. In an undisturbed stream, fines would be expected to only
accumulate in areas of locally reduced flow such as protected areas in macrophyte beds.
Aggradation of fines in other areas can be a sign that excessive erosion is occurring
within or upstream of the reach.
Because summer field crews consisted of students, graduate assistants, and professional
staff, effective training was necessary to ensure consistent data collection. Crew
members were trained on how to use the field sheets and definitions of categories. Then
a stream was visited, at which attributes of the stream habitat and development were
discussed to calibrate scoring techniques.
8
2.3. Sample metrics at chosen sample sites.
Following the development of sampling methods, data were collected at a total of 514
sites during the field seasons of 2006-2009 (Figure 9). Within some regions, it was not
possible to select 10 least or most disturbed sites due to the lack of available streams with
these disturbance ratings. Therefore once all targeted sites had been visited, we sampled
additional stream arcs with appropriate disturbance classes until 10 or all accessible arcs
were sampled in that region/disturbance class. Even with this extensive effort, certain
regions had fewer than ten sites sampled within each disturbance class (Table 2).
Sampled stream sites ranged in size from link number 1-410 (Shreve 1967) and channel
order 1-5 (Strahler 1957). Drainage areas (entire upstream catchments) ranged from
0.58-2260 km2. Regional disturbance levels varied somewhat throughout the state.
Streams in the northwest and southernmost portions of the state were relatively
undisturbed while streams in the central area of the state were highly impacted by
agriculture and in the northeast portion by urban landcover. Strip-mining was most
prevalent in the south-central portion of the state.
Annual variation in water level was evident in streams sampled in multiple years. The
summer of 2007 was extremely dry while the summers of 2008 and 2009 experienced
high amounts of rainfall and consequently, flooding and channel alteration in many areas.
JOB 3. Determine regions
3.1. Identify possible regionalization schemes (e.g., watersheds, natural divisions).
Illinois is a large state encompassing areas that vary topographically, geologically, and
historically. Therefore stream habitat and associated biotic assemblages may be expected
to vary regionally. Moreover human impacts and habitat response in streams to those
impacts can vary regionally (Smogor 2000), and a single set of metrics and metricscoring criteria may not reflect land use disturbances equally well statewide.
Regionalization of metric scoring can minimize the influence of natural variation in
metrics on the overall index score ensuring that differences in index scores reflect human
impacts. We investigated the relationship between habitat metrics and disturbance for
several alternative regionalization schemes (Figure 10). These included natural divisions
(Schwegman 1973), ecoregions (Woods et al. 2006), freshwater ecoregions (Abell et al.
2008), glacial boundaries, major watersheds, fish IBI regions (Smogor 2000), and a
stream classification (Holtrop and Dolan 2003).
The fish IBI regions were developed by Smogor (2000) to account for regional variability
in the composition of fish assemblages in least disturbed streams throughout the state
(Figure 10a.). He considered fish samples in several alternative regional groupings (e.g.,
prior IBI regions, physiographic regions, major river basins, Illinois EPA’s Aquatic Life
Management Units) to chose a set of regions in which metrics varied maximally,
therefore minimizing the potential for natural differences in metrics among regions to
confound interpretation of the IBI scores.
9
Freshwater ecoregions are constrained by watershed boundaries with delineation
primarily based on freshwater fish distributions (Figure 10b.). In developing the
freshwater ecoregions, Abell et al. (2008) used the best available regional information
describing freshwater biogeography, including influences of phylogenetic history,
paleogeography, and ecology.
Ecoregions are based on general similarity of ecosystems and were developed to be used
for implementation of ecosystem management across political boundaries (Figure 10c.;
Woods et al. 2006). Ecoregions are based on a hierarchal scale designed to “… stratify
the environment according to its probable response to disturbance, and recognize the
spatial differences in the capacities and potentials of ecosystems (Bryce et al. 1999).”
Illinois contains six level III ecoregions based on physiography, natural vegetation, soil,
surficial and bedrock geology, climate, land use and land cover, and regional
biogeography.
Glaciation is one of the most significant geologic processes to shape the landscape in
Illinois. Three major episodes have occurred in Illinois’ history: the Wisconsin, Illinois
and the Pre-Illinois episodes. Glacial erosion and deposition has changed the landscape
of Illinois by filling river valleys, changing the course of rivers, and creating new
landforms. Glacial boundaries represent the extent of glaciations from the major glacial
episodes in Illinois (Figure 10d; Illinois State Geological Society 1998).
Natural Divisions were developed to set the ground work for development of the Illinois
State Nature Preserves program (Figure 10e.). The fourteen natural divisions in Illinois
are based on differences in topography, glacial history, bedrock, soils and distribution of
flora and fauna (Schwegman 1973).
Major watersheds were delineated by the State Water Survey (Figure 10f; McConkey and
Brown 2000). Watershed boundaries follow topographic highs and a watershed is often
considered synonymous with a drainage basin or the land area that directly drains to a
common water body.
Finally, the utility of a stream classification based on stream size and gradient was
investigated (Holtrop and Dolan 2003; Table 9). Stream size was defined as channel link,
and slope was defined as percent gradient (Cordle et al. 2006, Brenden et al. 2006).
3.2. Identify degree to which metrics sampled at least-disturbed sites differ among
regions.
Multivariate Analysis of Variance (MANOVA) was used with selected candidate habitat
metrics to aid in determining the appropriate regionalization or stratification method
(Table 10). Box plots of the candidate metrics were used to determine which method
more consistently improved the ability to distinguish disturbance class beyond the
statewide pattern.
10
3.3. Select final regions.
Of the stratifications examined, ecoregions (Woods et al. 2006) and the stream
classification showed the strongest relations between the potential metrics (MANOVA,
Table 10). We selected ecoregions to regionalize metric scoring and incorporated size
and gradient into the regional scoring (Table 11; Figure 11). This approach is similar to
the development of other indexes used in Illinois (e.g., Smogor 2000).
Due to the limited area within Illinois, in several ecoregions we were not able to sample
(or find) adequate numbers of sites in each disturbance class within these ecoregions
(Table 11). For sites in the Mississippi Alluvial Plain and the Driftless Area we suggest
using the statewide scoring criteria as well as any available regional scoring for the area.
JOB 4. Select final metrics.
4.1 Select final metrics based on those that reflect levels of disturbance in each
region.
A total of 201 metrics were examined during the study ranging from direct measurements
to aggregations of metrics similar to some used by SHAP and QHEI (Appendix A).
Metrics considered addressed categories including: substrate type and quality, in-stream
cover types and amounts, channel quality and stability, riparian quality, amount of
erosion, pool and riffle quality, channel unit development, thalweg depth, and flow
variability. Analysis of variance (ANOVA), simple regression, box plots, and correlation
matrices were used to examine the differences in each metric among disturbance classes.
We used the following three criteria to narrow 201 metrics to 20. Metrics chosen
showed:
1. Statewide differences between disturbance classes (ANOVA, P 0.05).
2. Metric increases or decreases as expected from least- to moderately- to mostdisturbed conditions (box plots and correlation analysis (); Figure 12).
3. Metric values that varied between disturbance classes, but not within the least
disturbed class. (To determine this, we examined correlations between metric
scores and disturbance scores for the full range of sites (requirement P 0.05) and
of those, we examined correlations between metric scores and disturbance scores
(not classes) within just the least-disturbed sites (requirement P>0.05).
Twenty metrics that differed meaningfully among disturbance classes statewide were
selected from the original 201 (Appendix A) for further examination within the
ecoregions (Table 12). For each metric, data from the most disturbed class were
compared to data from the least disturbed class. If the metric was expected to increase
with increasing disturbance, the threshold was set at the 75th percentile of the least
disturbed data. The range of data from the most disturbed class was compared to this
threshold and the proportion of the data that fell above the threshold was calculated.
Likewise, if the metric was expected to decrease with increasing disturbance, the
threshold was set at the 25th percentile, and the proportion of most disturbed data falling
below this threshold was calculated. The calculated proportions were then examined.
11
Metrics with a proportion closer to one provide better discrimination between least and
most disturbed sites.
Additionally we made box plots of the least, moderate, and most disturbed data of the 20
candidate metrics by ecoregion. Several of the 20 metrics were similar in nature (e.g.,
Buffer-bare includes Average buffer), therefore we selected only one of similar metrics to
limit redundancy and to avoid weighting stream attributes unintentionally. The final five
metrics were chosen based on the box plots across all regions, ability to discriminate
between least and most disturbed stream sites, and lastly, with consideration of sampling
ease. The final metrics are: percent shade, buffer-bare, substrate ratio, large woody
debris, and the proportion of channel units that were riffles (Table 12).
JOB 5. Develop scoring criteria for each region.
We developed statewide and regional scoring criteria for wadeable Illinois streams using
the five metrics identified in Job 4. The full range of sites was treated as a single region
for developing statewide scoring criteria and sites were grouped by ecoregion and used to
develop regional scoring.
Potential outliers and influential data points were identified for each metric using three
methods: standardized deleted residuals (>2), centered leverage values (>4/n), and
DFBETA (change in regression coefficient resulting from the deletion of the ith case;
>2/sqrt n; SPSS 2008. Data that were identified as outliers by two of the three methods
were removed from further analysis (of that metric in that ecoregion only). This occurred
with less than 5% of data within each region.
Normal probability plots were examined for each candidate metric and three potential
covariates. Link, width, gradient, the proportion of large woody debris and the substrate
ratio were transformed with natural log. Buffer-bare, proportion of riffles and percent
shade were relatively normal and therefore not transformed.
5.1. Establish regional scoring criteria for each metric.
Earlier analysis (Job 3; MANOVA) indicated that stream size and gradient explained
some of the natural variation in several of our metrics. To address this within regions;
scatter plots of each metric were examined for meaningful variation with stream size
(link number, wetted width) and gradient using data from our least disturbed sites. The
covariate (link number, wetted width, or gradient) with the strongest relation to the metric
(highest R-squared value ≥ 0.10) was selected to assist with scoring the metric. When no
strong relation was found the mean value of the metric based on the least disturbed data
was used to set the scoring.
We plotted the regression line (or the mean value) of the metric against the covariate
using the least disturbed site data. This formed the lower bound of the highest scoring
class when the metric was negatively correlated with disturbance or the upper bound of
the highest scoring class when the metric was positively correlated with disturbance (e.g.,
substrate ratio). We then divided the area between the metric boundary and the minimum
12
value (or 90th percentile value for substrate ratio) into four equally spaced areas. The
resolution of the data for percent shade only allowed separation into four meaningful
classes so only three equally spaced areas were used.
We assigned a score of 5 to the area above the regression line of the least disturbed site
data for buffer-bare, large woody debris, and proportion of riffles. Since shading had
only four classes the area above the regression line was given a value of 4. The substrate
ratio metric was given a value of 5 below the regression line since this metric was
positively correlated with disturbance. We then sequentially decreased the value by one
for each adjacent region for all metrics. For consistency on how the regional metric
scoring is displayed those metrics that were not observed to be related to stream size or
gradient were plotted as lines with zero slope against the natural log of gradient
(Appendix C).
Metric values should be plotted on the appropriate regional, or statewide, scoring graph
to obtain metric scores (Appendix C). The overall index value is then determined as the
sum of individual metric scores and ranges from 5 – 24. Higher values indicate site
conditions more similar to those of least disturbed sites within their region.
JOB 6. Prepare final report.
6.1. Prepare final report including a “how to” manual.
A training manual “Procedure for Physical Habitat Measurements and Scoring of the
Illinois Habitat Index” was prepared and included with this final report (Appendix D).
6.2. Conduct a training workshop.
The training workshop was not conducted due to the index completion during winter.
Personnel from the INHS working on the coolwater stream (T-13) and mussel
communities (T-53) projects have been trained to collect data for use with the index
during sampling efforts in 2010. The IDNR is prepared and willing to conduct training
sessions for other interested groups.
Conclusions
We scored all sites that were visited during the study period that had the appropriate data
available (Figure 13). Mean and median index values were highest for least disturbed
sites (mean = 18.1, std dev = 3.2, median = 19.0, range 6 – 24, n = 146), and declined in
moderately disturbed (mean = 16.0, std dev = 4.7, median = 16.5, range 5 – 24, n = 210),
and most disturbed sites (mean = 15.3, std dev = 4.3, median = 15.0, range 5 – 24, n =
131). Sixty-four percent of moderately disturbed and seventy-five percent of most
disturbed sites scored lower than the least disturbed sites median index value although the
range of index values was relatively broad within each disturbance class. Sixty-one
percent of the index scores for most disturbed sites were below the median index value of
the moderately disturbed sites. These results suggest that the index has excellent
discriminatory power for separating least disturbed sites from most disturbed sites, and
reasonably good ability to differentiate moderately disturbed sites from least disturbed or
from most disturbed conditions.
13
Literature Cited
Abell, R., M. L. Thieme, C. Revenga, M. Bryer, M. Kottelat, N. Bogutskaya, B. Coad, N.
Mandrak, S. C. Balderas, W. Bussing, M. L. J. Stiassny, P. Skelton, G. R. Allen,
P. Unmack, A. Neseka, R. NG, N. Sindorf, J. Robertson, E. Armijo, J. V. Higgins,
T. J. Heibel, E. Wikramanayake, D. Olson, H. L. Lopez, R. E. Reis, J. G.
Lundberg, M. H. S. Perez, and P. Petry. 2008. Freshwater ecoregions of the
world: a new map of biogeographic units for freshwater biodiversity
conservation. BioScience 58(5): 403-414.
Allan, D. J., D. L. Erickson, and J. Fay. (1997). The influence of catchment land use on
stream integrity across multiple spatial scales. Freshwater Biology 37: 149-161.
Barbour, M. T., J. Gerritsen, B. D. Snyder, and J. B. Stribling. 1997. Revision to rapid
bioassessment protocols for use in streams and rivers: periphyton, benthic
macroinvertebrates, and fish. U.S. Environmental Protection Agency, Office of
Water, Washington, DC. EPA 841-D-97-002.
Brenden, T. O., R. D. Clark, Jr., A. R. Cooper, P. W. Seelbach, L. Wang, S. S. Aichele,
E. G. Bissell, and J. S. Stewart. 2006. A GIS framework for collecting,
managing, and analyzing multiscale landscape variables across large regions for
river conservation and management. Pages 49–73 in R. M. Hughes, L. Wang, and
P. W. Seelbach, editors. Landscape influences on stream habitats and biological
assemblages. American Fisheries Society, Special Publication 48, Bethesda,
Maryland.
Bryce, S. A., J. M. Omernik, and D. P. Larsen. 1999. Ecoregions – a geographic
framework to guide risk characterization and ecosystem management.
Environmental Practice 1(3): 141-155.
Cordle, L., K. S. Cummings, L. C. Hinz Jr., A. M. Holtrop, C. A. Phillips, J. W. Walk, J.
M. Epifanio. 2006. Development and Expansion of the Natural Resource Data
and Information Systems in Support of the Illinois Comprehensive Wildlife
Conservation Plan (Project: T-03-P-001). Illinois Natural History Survey
Technical Report 06/01.
Hedrick, L. B., S. A. Welsh, and J. T. Anderson. 2009. Influences of high-flow events
on a stream channel altered by construction of a highway bridge: a case study.
Northeastern Naturalist 16(3): 375-394.
Hite, R. L. and W. A. Bertrand. 1989. Biological stream characterization (BSC): A
biological assessment of Illinois stream quality. Special Report #13 of the Illinois
State Water Plan Task Force. IEPA/AC/89-275.
Holtrop, A. M. and C. R. Dolan. 2003. Assessment of streams and watersheds in
Illinois: Development of a stream classification system and fish sampling
protocols. Aquatic Ecology Technical Report 03/15. 28 pp.
14
Illinois Environmental Protection Agency. 1994. Quality assurance and field methods
manual. Illinois Environmental Protection Agency, Bureau of Water, Division of
Water Pollution Control, Planning Section. Springfield, Illinois.
Illinois State Geological Survey. 1998. Glacial Boundaries in Illinois. Champaign,
Illinois. Available at: http://www.isgs.uiuc.edu/nsdihome/webdocs/st-geolq.html
Karr, J. R., K. D. Fausch, P. L. Angermeier, P. R. Yant, and I. J. Schlosser. 1986.
Assessing biological integrity in running waters: a method and its rationale.
Illinois Natural History Survey, Special Publication 5, Champaign.
Lammert, M. and J. D. Allan. 1999. Assessing biotic integrity of streams: Effects of
scale in measuring the influence of land use/cover and habitat structure on fish
and macroinvertebrates. Environmental Management 23:257-270.
Luman, D. and M. Joselyn. 1996. Critical Trends Assessment Land Cover Database of
Illinois, 1991-1995 remote-sensing image. Illinois Natural History Survey,
Illinois State Geological Survey, Illinois Department of Natural Resources. IDNR
GIS Database /gisdb/county/<county_name>/landcov
McConkey, S. A. and K. J. Brown. 2000. Major Watersheds of Illinois. Illinois State
Water Survey Map Series 2000-01.
Platts, W. S., Megahan, W. F., Minshall, G. W. 1983. Methods for evaluating stream,
riparian, and biotic conditions. United States Department of Agriculture. General
Technical Report INT-138. 70 pp.
Rankin, E. T. 1989. The Qualitative Habitat Evaluation Index (QHEI): Rationale,
methods and application. Ohio Environmental Protection Agency, Division of
Water Quality Planning and Assessment, Ecological Assessment Section,
Columbus, Ohio.
Roth, N. E., J. D. Allan, and D. L. Erickson. 1996. Landscape influences on stream
biotic integrity assessed at multiple spatial scales. Landscape Ecology 11(3): 141156.
Schumm, S. A. 1960. The shape of alluvial channels in relation to sediment type; erosion
and sedimentation in a semiarid environment. U.S. Department of the Interior,
352-B, 17-60.
Schumm, S. A., M. D. Harvey, and C. C. Watson. 1984. Incised Channels:
Morphology, Dynamics, and Control. Southern Illinois University Carbondale.
Morris, Illinois. 200 pp.
15
Schwegman, J. E. 1973. Comprehensive Plan for the Illinois Nature Preserves System
Part 2 The Natural Divisions of Illinois. Illinois Nature Preserves Commission,
Springfield, Illinois. 31pp.
Shreve, R. L. 1967. Infinite topologically random channel networks. Journal of
Geology 75: 178-186.
Smogor, R. 2000. Draft manual for calculating Index of Biotic Integrity scores for
streams in Illinois. Prepared for: Illinois Environmental Protection Agency and
Illinois Department of Natural Resources. 23 pp.
SPSS. 2008. SPSS version 17. SPSS Inc., an IBM Company Headquarters. Chicago,
Illinois.
Stauffer, J. C. and R. M. Goldstein. 1997. Comparison of three qualitative habitat
indices and their applicability to prairie streams. North American Journal of
Fisheries Management 17:348-361.
Strahler, A. N. 1957. Quantitative analysis of watershed geomorphology. Transactions
of the American Geophyscial Union 38: 913-920.
Tiemann, J. 2004. Short-term effects of logging and bridge construction on habitat of
two Kansas intermittent streams. Transactions of the Kansas Academy of Science
107: 136-142.
Woods A. J., J. M. Omernik, C. L. Pederson, B. C. Moran. 2006. Level III and Level IV
ecoregions of Illinois. U.S. Environmental Protection Agency, National Health
and Environmental Effects Research Laboratory. Corvallis, Oregon. EPA/600/R06/104. 45pp.
16
Table 1. Land cover classes used for delineation of land cover types for analyses of disturbance in
whole and local watersheds and local riparian zones (Luman and Joselyn 1996).
Category Name
Urban and Built-Up Land
1 - High Density
2 - Med-High Density
3 - Medium Density
4 - Low Density
Category Description
All or most of the surface cover is comprised of impervious
material
Transitional between Medium and High Density; located in
Cook County only
Significant proportion of the surface cover is comprised of
impervious material
Small amount of surface area comprised of impervious
material mixed with other land cover
Transportation
5 - Major Roadways
6 - Active Railroads
7 - Abandoned Railroads
Major Highways updated 1992
Updated 1991
Updated 1991
Crop Land
8 - Row Crop
9 - Small Grains
10 - Orchards/Nurseries
Corn, soybeans, and other tilled crops
Wheat, oats, etc.
Cultivated tree crops
Grassland
11 - Urban Grassland
12 - Rural Grassland
Parks, residential lawns, golf courses, cemeteries, and other
open space
Pastureland, grassland, waterways, buffer strips, CRP
Wooded and Forested Land
13 - Deciduous
Undifferentiated broadleaf deciduous, closed canopy
14 - Deciduous
Undifferentiated broadleaf deciduous, open canopy
15 - Coniferous
Undifferentiated
16 - Open Water
17 - Perennial Streams
Wetland
18 - Shallow Marsh/Wet Meadow
19 - Deep Marsh
20 - Forested Wetlands
21 - Swamp
22 - Shallow Water Wetlands
23 - Barren Land
No extra description given in the metadata
No extra description given in the metadata
No extra description given in the metadata
No extra description given in the metadata
No extra description given in the metadata
quarries, sandy beaches, exposed soil surfaces, etc.
17
Table 2. Total number of sites sampled by IBI region and disturbance class.
IBI
Region
1
2
3
4
5
6
7
8
9
10
11
12
13
Total
Disturbance Class
Least Moderate Most
7
9
9
12
18
10
10
12
10
9
15
10
7
15
11
7
32
11
14
22
18
13
16
12
14
24
8
14
8
16
14
28
9
20
16
5
11
13
5
152
228
134
18
Total
25
40
32
34
33
50
54
41
46
38
51
41
29
514
Table 3. Metrics and scores comprising Illinois’ Stream Habitat Assessment Procedure (SHAP). The
overall index value is determined as the sum of individual metric scores and ranges from 5 – 24.
Higher values indicate site conditions more similar to those of least disturbed sites within their
region.
Metric
Excellent
Substrate and Instream Cover
Bottom Substrate
16-20
Deposition
10-12
Substrate Stability
13-16
Instream Cover
10-12
Pool Substrate
16-20
Good
Fair
11-15
7-9
9-12
7-9
11-15
6-10
4-6
5-8
4-6
6-10
1-5
1-3
1-4
1-3
1-5
Channel Morphology and Hydrology
Pool Quality
13-16
Pool Variability
13-16
Channel Alteration
7-8
Channel Sinuosity
10-12
Width: Depth Ratio
13-16
Hydrologic Diversity
10-12
9-12
9-12
5-6
7-9
9-12
7-9
5-8
5-8
3-4
4-6
5-8
4-6
1-4
1-4
1-2
1-3
1-4
1-3
Riparian and Bank Features
Canopy Cover
Bank Vegetation
Immediate Land Use
Flow-Related Refugia
7-9
9-12
5-6
7-9
4-6
5-8
3-4
4-6
1-3
1-4
1-2
1-3
10-12
13-16
7-8
10-12
19
Poor
Table 4. Metric comprising Ohio’s Qualitative Habitat Evaluation Index (QHEI; gradient omitted).
Metrics
Channel Morphology
Sinuosity
Development
Channelization
Stability
Riparian Zone and Bank Erosion
Riparian Width
Floodplain Width
Bank Erosion
Pool/Glide and Riffle Run Quality
Maximum Depth of Pools
Morphology
Current Velocity
Riffle/Run Depth
Riffle/Run Substrate
Riffle/Run Embeddedness
In-stream Cover
Cover Type
Cover Amount
Scores
High (4), Moderate (3), Low (2), None (1)
Excellent (7), Good (5), Fair (3), Poor (1)
None (6), Recovered (4), Recovering (3), Recent (1)
High (3), Moderate (2), Low (1)
Wide (4), Moderate (3), Narrow (2), Very Narrow (1),
None (0)
Forest/Swamp/Woods (3), Shrub/Old field (2),
Residential/Park (1), Conservation tillage/Fenced
pasture (1), Urban/Industrial (0), Open pasture/Row
crops (0), Mining/Construction (0)
None/little (3), Moderate (2), Heavy/Severe (1)
>1m (6), 0.7-1.0 m (4), 0.4-0.7 m (2), 0.2-0.4 m (1),
<0.2 m (0)
Pool width > riffle width (2), pool width = riffle width
(1), pool width < riffle width (0)
Eddies (1), Fast (1), Moderate (1), Slow (1),
Torrential (-1), Interstitial (-1), Intermittent (-2_
Max >50 cm (4), Max 10-50 cm (3), Max 5-10 cm
(1), Max <5 cm (0)
Stable (2), Moderate to stable (1), Unstable (0)
None (2), Low (1), Moderate (0), Extensive (-1), No
Riffle (0)
Undercut bank (1), Overhanging vegetation (1),
Shallows (1), Rootmats (1), Deep pools (2), Rootwads
(1), Boulders (1), Oxbows (1), Aquatic macrophytes
(1), Logs/woody debris (1)
Extensive (1), Moderate (7), Sparse (3), Nearly absent
(1)
20
Table 4. cont. Metric comprising Ohio’s Qualitative Habitat Evaluation Index (QHEI; gradient
omitted).
Metrics
Substrate
Substrate Type
Substrate Origin
Substrate Quality: Silt
Substrate Quality: Embeddedness
Scores
Boulder slabs (10), Boulders (9), Cobbles (8), Gravel
(7), Sand (6), Silt (2), Muck (2), Hardpan (4),
Bedrock (5), Detritus (3), Artificial (0)
Limestone (1), Tills (1), Wetlands (0), Hardpan (0),
Sandstone (0), Riprap (0), Lacustrine (0), Shale (-1),
Coal fines (-2)
Heavy (-2), Moderate (-1), Normal (0), Silt free (2)
Extensive (-2), Moderate (-1), Normal (0), None (1)
21
Table 5. Candidate metrics that were collected by field staff for metric development (Appendix B).
Scale refers to whether the metric was recorded for each individual channel unit (e.g., run, riffle,
pool, or transitional), for the entire sampling reach, or both.
Metric
Buffer Width
Riparian Type
Stream Bank Vegetation
Predominant Channel Type
Predominant Substrate
Predominant Flow
Shading of Water Surface
Thalweg Depths
Channel Evolution Stage
Water Level
Stream Modifications
Wetted Width
Thalweg Depth
Channel Unit Type
Cover
Substrate Embeddedness
Depth of Fines as Bottom
Cover
Cross Section Depths
Max depth
Definition
Width of the undeveloped buffer on each side
of the stream
Type of vegetation growing in the buffer zone
Type of vegetation growing on the stream
banks
Pool, Riffle, or Run
Most abundant type of substrate (see Table 6)
Fast, Moderate, Slow, or No detectable flow
Completely, mostly, half, most light, all light
10 approximately equidistant depths taken
Per Schumm et al. (1984)
Rising, base flow, decreasing or pooled
Any human perturbations are noted
Taken at the downstream, mid and upstream
points
Taken at the downstream, mid and upstream
points
Lateral pool, mid-channel pool, riffle, run or
transitional
Scale
Reach
Abundance of 9 cover types (see Table 3)
Only applied to sites with dominant substrate
as fine gravel and larger
Recorded as None, 1-25 mm, 25-50, 50-75,
and >75 mm
Eight depths are taken across pools from left to
right bank facing upstream
Deepest point of a unit (measured in all units)
Unit
Unit
22
Reach
Reach
Reach
Both
Both
Reach
Reach
Reach
Reach
Reach
Reach
Reach
Unit
Unit
Unit
Unit
Table 6. Substrate and bottom type categories used in stream habitat assessment taken from Illinois’
Stream Habitat Assessment Procedure (SHAP; IEPA 1994).
Substrate type
Bedrock
Hardpan
Silt
Sand
Fine Gravel
Gravel
Cobble
Slab Boulder
Boulder
Particle size
Solid rock
Compacted fines
<0.062 mm
0.062-2 mm
2-8 mm
8-64 mm
64-256 mm
>256 mm
>256 mm
23
Table 7. Buffer categories used in stream habitat assessment.
Buffer Size
None
Very Narrow
Narrow
Moderate
Wide
Very Wide
Width of Buffer
<1 m
1-5 m
5-10 m
10-50 m
50-100 m
>100 m
24
Table 8. Cover definitions for channel units. Amount of each cover type is estimated as none, sparse,
intermediate or abundant.
Cover Type
Aquatic macrophytes
Undercut bank
Overhanging
vegetation
Rootwads
Rootmats
Boulder
Large woody debris
(LWD)
Aggregate of woody
debris
Definition
Non-terrestrial, emergent, floating, or submerged
macrophytes, not including algae
Bank with a cavity below the waterline
Plant foliage suspended over the wetted channel and within
one meter of the water’s surface
Root mass from a tree that is in wetted channel and
diverting water flow
Fibrous roots from trees and other plants extending into the
wetted channel
Substrate particle larger than 250 millimeters (modified
Wentworth scale) along the second shortest axis
Woody material (e.g. log or tree) with a diameter greater
than 10 cm, length greater than 1 meter, in wetted channel
and diverting water flow
Two or more LWD, must be in wetted channel and
diverting water flow
25
Table 9. Stream classes were determined by gradient and size. Gradient was measured as percent
slope. Stream size was measured by link number. Table 9a provides the ranges for size and gradient
with in each class. Every stream arc was given two numbers; one for the corresponding gradient
group and one for size. These number were combined categorically (e.g., a stream a with link
number 25 and a gradient of 0.0012 would be put in the 21 category for stream class). Table 9b
provides the number of sites sampled in each disturbance class for each stream type.
Table 9a.
Group
Description
Gradient Percent Slope
1
0-0.001364
2
0.001365-0.003778
3
>0.003778
Size
1
2
3
4
5
6
7
Link Number
0-20
21-150
151-180
181-725
726-1300
1301-6500
>6500
Table 9b.
Stream Class
11
12
13
21
22
23
31
41
Total
Least Moderate
33
68
45
42
30
30
19
54
13
16
10
9
1
6
1
3
152
228
26
Most
35
34
17
23
11
10
0
4
134
Total
136
121
77
96
40
29
7
8
514
Freshwater
Ecoregions
Major
Watersheds
Natural
Divisions
Glacial
Boundaries
Ecoregions
Size Gradient
Class
Dependent Variable
Proportion of runs
Proportion of riffles
Average buffer width
Average riparian type
Buffer riparian
Average Buffer Ranked
Riparian QHEI
Substrate stability
Percent shade
Thalweg max:min
Thalweg mean:max
Thalweg range
Max Depth in Units
Pool Quality
Pool WOOD
Count of cover
Cover structure
Proportion of aquatic
macrophytes
Proportion of LWD
Proportion of WOOD
IBI Regions
Table 10. Model significance results reported for the Multivariate Analysis of Variance (MANOVA)
run on candidate regionalization schemes using potential index metrics. Numbers with a box around
them and highlighted yellow (grey) indicate a significance level of p≤0.05. Dependent variables are
defined in Appendix A.
.055
.710
.492
.089
.232
.754
.100
.399
.916
.172
.834
.278
.695
.265
.813
.800
.594
.895
.748
.313
.195
.475
.565
.079
.262
.830
.390
.944
.552
.326
.476
.722
.272
.666
.588
.670
.777
.156
.603
.554
.767
.243
.595
.128
.281
.497
.875
.513
.702
.401
.288
.205
.543
.507
.064
.419
.756
.756
.673
.503
.287
.726
.107
.134
.228
.295
.127
.551
.139
.421
.395
.240
.317
.439
.309
.253
.461
.664
.283
.375
.607
.202
.761
.219
.787
.004
.043
.310
.241
.023
.037
.011
.456
.578
.030
.382
.851
.686
.874
.985
.444
.390
.726
.274
.560
.484
.696
.114
.779
.005
.072
.641
.025
.024
.440
.058
.000
.155
.752
.186
.141
.112
.924
.176
.153
.000
.873
.458
.599
.915
.747
.550
.693
.946
.232
.463
.103
.801
.000
.226
27
Table 11. Number of sites sampled in each disturbance class in each ecoregion.
Ecoregion
Central Corn Belt Plains
Driftless Area
Interior Plateau
Interior River Valleys and Hills
Mississippi Alluvial Plain
Southeastern Wisconsin Till Plain
Total
Disturbance Class
Least Moderate Most
33
107
63
7
8
9
15
12
6
86
94
53
1
1
1
10
6
2
152
228
134
28
Total
203
24
33
233
3
18
514
Table 12. List of the final candidate metrics narrowed down from the original 200. The final five
metrics used are listed first.
Metric Name
Percent shade
Metric Description
Shade recorded as a percentile category ranging from no
shade to completely shaded [0-25-50-75-100]
Buffer / bare
Average of buffer minus average amount of bare soil on the
banks + 3 (range 0-8)
Proportion of large
Proportion of logs and aggregate large woody debris in all
woody debris cover
units except riffles
Proportion of riffles
Proportion of units that are labeled as riffles in the reach
Ratio dominant next size Of the dominant and next dominant substrate for the reach,
ratio of the largest to the smallest (substrate sizes assigned
from Table 6)
Pool wood
Sum of the sums of large woody debris + aggregate wood +
rootwads for each pool divided by 3*number of pools in reach
Substrate stability
Sum of the proportions of boulder and cobble + aquatic
macrophytes
Proportion of aquatic
Proportions of aquatic macrophytes as cover in all units
macrophytes
except riffles
Wood in pools
Proportion of logs, woody debris and root wads in all pools
Count of cover
Count of the number of cover types in the reach
Average buffer
Sum (left buffer width + right buffer width) divided by 2
Average riparian type
Coded riparian types averaged across the left and right banks.
Buffer riparian
Sum of coded (Average buffer width + Average riparian type)
Cover structure
Count of left and right values (trees + herbaceous + wood +
bedrock) from the stream reach bank cover
Channel development
Sum (Average buffer + Average riparian + Channel
evolution)
Proportion of runs
Proportion of units that are runs in the reach
Pool quality
An integrated measure based on pool type, depth, cover, and
development. See Appendix C.
Max of max depth unit
The deepest maximum depth across all units
Thalweg max:min
Ratio of the largest to the smallest depths (max depth divided
by min depth)
Thalweg mean:max
The average thalweg depth divided by the max thalweg depth
Thalweg range
The maximum thalweg depth minus the min thalweg depth
29
Figure 1. Sketch of a local watershed, total upstream catchment, and riparian zone. Local
watersheds pertain to area draining directly to the specific stream arc, while the catchments include
all upstream drainage area. Riparian zone included a 150 m buffer centered on the stream arc. The
riparian zone did not extend up into the total catchment.
30
Figure 2. Distribution map of disturbance ratings for proportions of disturbed land in the whole
watersheds of Illinois streams. Stream arcs are color coded by disturbance rating: 1-5 = blue, 6-10 =
green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate less disturbance of this type.
31
Figure 3. Distribution map of disturbance ratings for the volume of impounded water in the whole
watershed of each stream arc. Stream arcs are color coded by disturbance rating: 1 = grey, 2-5 =
blue, 6-10 = green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate less disturbance of
this type.
32
Figure 4. A map showing an example of the proportion of strip-mined land (gray) in each watershed
assessed (black outlines in the inset). Proportions were calculated by dividing the area of each
watershed in strip-mined land by the total area of that watershed. Proportions were used to
determine disturbance classes for each disturbance type (Figure 5).
33
Figure 5. Distribution map of disturbance ratings for strip-mined land affecting Illinois streams.
Stream arcs are color coded by disturbance rating: 1 = grey, 2-5 = blue, 6-10 = green, 11-15 = yellow,
16-20 = red. Smaller numbers ratings indicate less disturbance of this type.
34
Figure 6. Distribution map of disturbance ratings for undisturbed land uses in the riparian zones of
Illinois streams. Stream arcs are color coded by disturbance rating: 1-5 = blue, 6-10 = green, 11-15 =
yellow, 16-20 = red. Smaller numbers ratings indicate less disturbance of this type.
35
Figure 7. Distribution map of disturbance ratings for the density of road crossing in the local
watershed for Illinois streams. Stream arcs are color coded by disturbance rating: 1-5 = blue, 6-10 =
green, 11-15 = yellow, 16-20 = red. Smaller numbers ratings indicate less disturbance of this type.
36
Figure 8. Map depicting total disturbance classes for stream arcs in Illinois. Blue streams are least
disturbed (lower 15th percentile), green are moderately disturbed and red streams are most disturbed
(upper 90th percentile).
37
Figure 9. Map of Illinois showing the location of all sampled sites. Blue circles represent sample
locations on streams that are least disturbed, green are moderately disturbed and red circles are
sample locations on most disturbed stream arcs.
38
Figure 10. Maps delineating the regionalization schemes considered to address regional variation in
habitat measures: a. Fish IBI regions, b. Freshwater ecoregions, c. Ecoregions of Illinois, d. Glacial
boundaries, e. Natural Divisions, and f. major watersheds.
39
Figure 11. Map of Illinois delineated by ecoregions (Woods et al. 2006) and showing the location of
all sampled sites. Blue circles represent sample locations on streams that are least disturbed, green
are moderately disturbed and red circles are sample locations on most disturbed stream arcs.
40
Figure 12. Proportion of large woody debris (p_LWD) by disturbance class.
41
Figure 13. Range of index scores for each disturbance class. A lower index score indicates a less
disturbed stream. Index scores range from 5-24.
42
Appendix A. A list of all candidate metrics examined.
ID Candidate Metric
Substrate - Type
Description of the metric
1
2
3
4
5
6
7
Boulder/cobble
Gravel
Sand
Hardpan
Silt
Bedrock
Proportion of boulder/cobble
8
Proportion of gravels
9
Proportion of sand
10
Proportion of hardpan
11
Proportion of silt
12
Proportion of bedrock
13
Predominant substrate in the unit
14
15
Predominant substrate in the reach
Dominant substrate
Number of units in which boulders or cobble were listed as dominant
Number of units in which gravel or fine gravel were listed as dominant
Number of units in which sand was listed as dominant
Number of units in which hardpan was listed as dominant
Number of units in which silt was listed as dominant
Number of units in which bedrock was listed as dominant
Number of units in which boulders or cobble were listed as dominant divided by total
number of units
Number of units in which gravel or fine gravel were listed as dominant per reach
divided by total number of units
Number of units in which sand was listed as dominant per reach divided by total
number of units
Number of units in which hardpan was listed as dominant per reach divided by total
number of units
Number of units in which silt was listed as dominant per reach divided by total
number of units
Number of units in which bedrock was listed as dominant per reach divided by total
number of units
Substrate that had the highest proportional value for units
(if unit has a tie for the dominant substrate, cell is left blank)
Taken directly from reach data
Substrate recoded small to large:
Substrate
Numerical Code
Silt
1
Sand
2
Hardpan
3
Fine gravel
4
Gravel
5
Cobble
6
Boulder
7
Slab Boulder
7
Bedrock
8
16
17
Next dominant substrate
Substrate QHEI
18
Dominant substrate QHEI
Substrate recoded small to large, same as Dominant substrate
Sum(Dominant substrate + Next dominant substrate + Average embeddedness +
Average of deepest fines)
Substrate recoded:
Substrate
Numerical Code
Clay
2
Silt
2
Hardpan
4
Bedrock
5
Sand
6
Fine gravel
7
Gravel
7
Cobble
8
Boulder
10
Slab Boulder
10
43
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
19
20
Next dominant substrate QHEI
Substrate QHEI2
21
Dominant substrate for the
dominant unit type
Substrate recoded same as Dominant substrate QHEI
Sum(Dominant QHEI + Next dominant QHEI + Average embeddedness + Average
of deepest fines)
Most commonly chosen substrate type in all units marked in reach as dominant unit
(e.g. If predominant unit type is pool, then only consider pools.)
Substrate - Quality
22
Recoded substrate class
Substrate recoded:
Substrate
Clay
Silt
Sand
Hardpan
Fine gravel
Gravel
Cobble
Boulder
Slab Boulder
Bedrock
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Proportion of soft substrate
Proportion of coarse substrate
Deepest fine
Deepest fine
(no silt-dominant units)
Deepest fine run
Deepest fine run
(no silt-dominant units)
Deepest fine riffle
Deepest fine riffle
(no silt-dominant units)
Deepest fine pool
Deepest fine pool
(no silt-dominant units)
Pool (silt-dominant units only)
Proportion of pool
(silt-dominant units only)
Pool silt both
Proportion of pool silt both
39
40
Number of units (silt-dominant
units only)
Proportion of units
(silt-dominant units only)
Number of units silt both
Proportion of units silt both
41
Number of units not embedded
42
Proportion of units not embedded
43
Proportion of macrophytes
38
Numerical Code
1
1
2
3
4
4
5
5
5
6
Proportion of units with dominant substrate as sand, silt, of hardpan
Proportion of units with dominant substrate as boulder, cobble, gravel, or bedrock
Deepest measure of fines across all units in the reach
Deepest measure of fines recalculated to include only units that do not have silt
marked as dominant substrate
Deepest measure of fines across all runs in the reach
Deepest measure of fines across all runs in the reach not including runs with silt as
dominant substrate
Deepest measure of fines across all riffles in the reach
Deepest measure of fines across all riffles in the reach not including riffles with silt
as dominant substrate
Deepest measure of fines across all pools in the reach
Deepest measure of fines across all pools in the reach not including pools with silt as
dominant substrate
Number of pools with silt marked as the dominant substrate
Number of pools with silt as dominant substrate divided by total number pools
(if there are no pools in the reach, the cell is left blank)
Number of pools with silt marked as the dominant or subdominant substrate
Number of pools with silt as dominant or subdominant substrate divided by total
number of pools (if there are no pools in the reach, the cell is left blank)
Number of units with silt marked as the dominant substrate
Number of units with silt as dominant or subdominant divided by total number units
Number of units with silt marked as the dominant or subdominant substrate
Number of units with silt as dominant or subdominant divided by total number of
units
Number of units in reach marked as not embedded
(cell is left blank if all units are n/a)
Number of units not embedded divided by total number units.
(cell is left blank if all units are n/a)
Number of units that have any macrophyte cover divided by total number of units
44
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
44
45
Average of deepest fines
Average of embeddedness
46
Average of percent embed
47
48
Substrate stability
Dominant substrate size
Average of deepest fines across the units
Average of the embeddedness across the units (embeddedness is scored 0 = 0%,
1 = 1-25%, 2 = 26-50%,3 = 51-75%,4 = 76-100%)
Average of the embeddedness across the units (embeddedness is scored
0,25,50,75,100)
Sum of the Proportions of boulder and cobble + Proportion of aquatic macrophytes
Dominant substrate from reach datasheet recoded using sizes instead of numbers:
Substrate
Numerical Code
Clay
0.001
Hardpan
0.001
Silt
0.05
Sand
1.00
Fine gravel
5.00
Gravel
36.00
Cobble
160.00
Boulder
256.00
Slab Boulder
256.00
Bedrock
500.00
49
Next dominant substrate size
50
52
Average of dominant substrate
size
Average of next dominant
substrate size
Average substrate size
53
Ratio dominant next size
54
55
56
57
58
Proportion of
boulder/cobble/gravel
Number of dominant substrate
Number of all substrate
Proportion of size substrate
Dominant substrate recoded
59
Next Dominant substrate recoded
60
Recoded substrate ratio
51
Next dominant substrate from reach datasheet recoded using sizes instead of
numbers (same as Dominant substrate size)
Dominant substrate size from unit averaged across all units in the reach
Next dominant substrate size from unit averaged across all units in the reach
Dominant substrate size and next dominant substrate size from unit then both (all)
are averaged across all units in the reach
Of the dominant and next dominant substrate for the reach, ratio of the largest to the
smallest
Sum(Proportion of boulder and cobble + Proportion of slab boulder + Proportion of
cobble + Proportion of gravel)
Count of the different types of substrate checked as dominant
Count of the different types of substrate checked as dominant and next dominant
Substrates multiplied by their size, then summed across the reach
Dominant substrate for the reach recoded so numbers are in order of size:
Substrate
Numerical Code
Silt
1
Clay
3
Hardpan
3
Sand
4
Fine gravel
5
Gravel
6
Cobble
7
Boulder
8
Slab Boulder
9
Bedrock
10
Next dominant substrate for the reach recoded so numbers are in order of size (same
as Dominant substrate recoded)
Of both the dominant and next dominant substrate for the reach, ratio of the largest to
the smallest using the recoded numbers as listed for Dominant substrate recoded
45
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
In-stream cover-type
Description of the metric
61
62
Number of cover types reach
Number of cover types runs
63
Number of cover types pools
64
Proportion of units with other
65
Proportion of junk
66
Proportion of undercut banks
67
68
Proportion of overhanging
vegetation
Proportion of rootwad cover
69
Proportion of boulder cover
70
Proportion of large woody debris
cover
Proportion of rootmat cover
75
Proportion of undercut banks and
overhanging vegetation
Proportion of aquatic macrophytes
76
Number of pools >70 cm
Count of the different cover types marked (number 0-9, not frequency)
Count of the different cover types marked in only the runs
(number 0-9, not frequency)
Count of the different cover types cited in only the pools
(number 0-9, not frequency)
Proportion of units with "other" as a cover type in a reach
(total number of units marked divided by total possible units)
Proportion of unite with “other” that was labeled as some sort of human litter
(total number of units marked divided by total possible units)
Proportion of undercut banks as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of overhanging vegetation as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of rootwads as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of boulders as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of logs or woody debris + aggregate large woody debris as cover in all
units except riffles (total number of units marked divided by total possible units)
Proportion of rootmats as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of overhanging vegetation + rootmats as cover in all units except riffles
(total number of units marked divided by total possible units)
Proportion of logs or woody debris + aggregate large woody debris + rootwads as
cover in all units except riffles (total number of units marked divided by total
possible units)
Proportion of undercut banks + over hanging vegetation as cover in all units except
riffles (total number of units marked divided by total possible units)
Proportion of aquatic macrophytes as cover in all units except riffles
(total number of units marked divided by total possible units)
Number of pools >70 cm (70 cm is used in QHEI as a "quality" pool)
77
Number of pools >50 cm
Number of pools >50 cm
78
Proportion of pools >70 cm
79
Proportion of pools >70 cm
(all units)
Proportion of pools >50 cm
Proportion of pools >70 cm deep (calculated with only "pool" units: number of pools
>70 cm divided by the total number of pools)
Proportion of pools >70 cm deep (calculated with all units in the reach: the number
of pools >70 cm was divided by the total number of units)
Number of pools >50 cm divided by total number of pools
82
Proportion of pools >50 cm
(all units)
Number of runs >70 cm
Number of pools >50 cm divided by total number of units (calculated with all units
in the reach: the number of pools >50 cm was divided by the total number of units)
Number of runs >70 cm
83
Number of runs >50 cm
Number of runs >50 cm
84
Proportion of runs >70 cm
Number of runs >70 cm divided by total number of runs
85
Proportion of runs >70 cm
(all units)
Proportion of runs >50 cm
Number of runs >70 cm divided by total number of units (calculated with all units in
the reach: the number of runs >70 cm was divided by the total number of units)
Number of runs >50 cm divided by total number of runs
88
Proportion of runs >50 cm
(all units)
Number of units >70 cm
Number of runs >50 cm divided by total number of units (calculated with all units in
the reach: the number of runs >50 cm was divided by the total number of units)
Number of units >70 cm
89
Number of units >50 cm
Number of units >50 cm
71
72
73
74
80
81
86
87
Proportion of overhanging
vegetation and rootmat cover
Proportion of wood
46
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
90
Proportion of units >70 cm
Number of units >70 cm divided by total number of units
91
Proportion of units >50 cm
Number of units >50 cm divided by total number of units
In-stream cover-amount
92
93
94
Proportion of units with no cover
Proportion of units with some
cover
Proportion of 0s for cover
95
Proportion of 1s for cover
96
Proportion of 2s for cover
97
Proportion of 3s for cover
98
Pool overhanging-root mats
99
Pool wood
100
Run overhanging-root mats
101
Run wood
102
Riffle overhanging-root mats
103
Riffle wood
104
105
106
Proportion of total cover
Count of cover
Cover QHEI
Number of units in each reach with no cover divided by total number units
Proportion of units in each reach that have at least some cover marked.
Number of 0s marked divided by the possible number of times "0" could have been
marked ( = 9 * number of units)
Number of 1s marked divided by the possible number of times "1" could have been
marked ( = 9 * number of units)
Number of 2s marked divided by the possible number of times "2" could have been
marked ( = 9 * number of units)
Number of 3s marked divided by the possible number of times "3" could have been
marked ( = 9 * number of units)
Sum of (Overhanging vegetation + root mats) for each pool, then the sums are
averaged across the reach
Sum of the sums of large woody debris + aggregate wood + rootwads for each pool
divided by 3*number of pools in reach
Sum of (Overhanging vegetation + root mats) summed for each run, then the sums
are averaged across the reach
Sum of (Large woody debris + Aggregate wood + Rootwads) summed for each run,
then the sums are averaged across the reach
Sum of (Overhanging vegetation + root mats) summed for each run, then the sums
are averaged across the reach
Sum of (Large woody debris + Aggregate wood + Rootwads) summed for each run,
then the sums are averaged across the reach
All numbers circled are summed then divided by [(3 * 9) * number of units]
Count of the number cover types per reach
Sum of (Proportion of undercut + Proportion of overhanging + Proportion of
rootmat + Proportion of rootwad + Proportion of boulder + Proportion of aquatic
macrophytes + Proportion of large woody debris + Proportion of pools>70cm)
Channel quality/stability
107
Channel evolution
Coded 1-5:
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
108
Chan evolution class
Numerical Code
1
3
3
4
5
Channel evolution recoded 1,2,3:
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
47
Numerical Code
3
1
1
2
3
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
109
Channel evolution recoded 1,2,3,4:
Chan evolution class2
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
110
Chan evolution class3
Chan evolution class4
Chan evolution class5
Numerical Code
1
2
3
3
4
Channel evolution recoded 1,2,3:
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
112
1
2
3
4
1
Channel evolution recoded 1,2,3,4:
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
111
Numerical Code
Numerical Code
1
2
3
3
2
Channel evolution recoded 1,2,3,4:
Channel
Evolution
Stable (1)
Incising (2)
Widening (3)
Stabilizing (4)
Stable (5)
Numerical Code
1
2
3
4
2
113
114
Width : depth
Shading
Average of the upper, middle, and downstream width : depth ratios
Coded:
Shading
Numerical
Code
Lack of canopy; full sunlight reaching the water
0
Most water surface receiving sunlight
1
Half water surface shaded, half full sunlight
2
Water mostly shaded with some sunlight
3
Water surface completely shaded
4
115
Percent shade
Shading recoded:
Shading
Lack of canopy; full sunlight reaching the water
Most water surface receiving sunlight
Half water surface shaded, half full sunlight
Water mostly shaded with some sunlight
Water surface completely shaded
48
Numerical
Code
0
25
50
75
100
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
116
117
118
Amount circled for “Bare” -average of left and right stream banks (range 0-3)
0 = no, 1 = yes
Sum (Average buffer + Average riparian + Channel evolution)
Average bare
Channelized
Channel development
Riparian quality /erosion
119
Left buffer
Coded:
Buffer description
None (<1m)
Very Narrow (1-5m)
Narrow (5-10m)
Moderate (10-50m)
Wide (50-100m)
Very Wide (<100m)
Numerical Code
0
1
2
3
4
5
120
121
122
123
124
125
126
Right buffer
Min buffer
Max buffer
Average buffer
Buffer riparian
Buffer bare
Left buffer ranked
Coded the same as Left buffer
Smaller width of the right or left buffer width
Larger width of the right or left buffer width
Sum (Left buffer width + Right buffer width) divided by 2
Sum of coded (Average buffer width + Average riparian type)
Aveerage buffer minus average bare + 3 (range 0-8)
Left buffer recoded:
Buffer description
Numerical Code
None (<1m)
0
Very Narrow (1-5m)
5
Narrow (5-10m)
10
Moderate (10-50m)
50
Wide (50-100m)
100
Very Wide (<100m)
150
127
128
129
130
131
Right buffer ranked
Average buffer ranked
Adjacent land use
Bank erosion
Bank stability
132
Cover structure
133
Average riparian type
Coded same as Left buffer ranked
Sum (Left buffer ranked + Right buffer ranked) divided by two
0 = forest, 1 = urban, 2 = agriculture (averaged across the left and right banks)
Sum of left and right bare bank value from the stream reach bank cover
Sum of left and right values (trees + herbaceous + wood - bare) from the stream
reach bank cover
Count of left and right values (trees + herbaceous + wood + bedrock) from the
stream reach bank cover
Coded riparian types averaged across the left and right banks. Coded as:
Riparian description
Numerical Code
If Buffer width = 0
0
Herbaceous
1
Mixed
2
Woody Shrubs
3
Trees
4
134
135
136
Bank erosion ranked
Bank stability ranked
Riparian QHEI
Sum of left and right “bare” values bank from the stream reach bank cover
Sum of left and right stream bank values (trees + herbaceous + wood - bare)
Sum (Average buffer + Average riparian type + Channel evolution class)
49
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Pool/riffle quality
Description of the metric
137
138
Proportion of units that are labeled as a riffle in the reach
Proportion of units that are riffles and are >10 cm deep divided by total number units
139
140
141
142
143
144
145
146
147
148
149
150
151
152
Proportion of riffles
Proportion of riffle >10cm all
units
Number of lateral pools
Number of mid-channel pools
Number of pools
Number of riffles
Pool max average
Pool min average
Pool mean average
Pool max variance
Pool mean variance
Count units not pools
Proportion of pools
Proportion of mid-channel pools
Proportion of lateral pools
Pool variance score
Number of lateral pools in each reach
Number of mid-channel pools in each reach
Total number of pools in each reach
Number of riffles in each reach
Average of the max depth across all pools in the reach
Average of the min depth across all pools in the reach
Average of the mean depth across all pools in the reach
Variance of the max depth across all pools in the reach
Variance of the mean depth across all pools in the reach
Number of units that are not pools
Number of pools in the reach divided by number units in reach
Proportion of units that are mid-channel pools
Proportion of units that are lateral pools
Pool Description
No pools in the reach
The whole reach is one pool, or all channel units are marked as
mid-channel pools
There are more mid-channel pools than lateral pools
There are more lateral pools than mid-channel pools
The number of mid-channel and lateral pools is the same
153
Mean range of pool cross-sections
154
155
156
Max riffle depth average
Average max depth riffles
Pool : riffle ratio
157
158
Average of pool variance
Pool quality
Numerical
Code
0
1
2
3
4
Average of max depth of all pools' cross-sections in the reach minus the average of
the minimum depth of all pools' cross-sections in the reach
Max of the average riffle depth in the reach
Average of the max depth in riffles
Number of pools divided by number of riffles
Average of the variances in the cross-section depths in each pool across the reach
An integrated measure based on pool type, depth, cover, and
development. Based on a sum of scores:
One point is given for each criteria met, range 0-6. If there are no pools in
the reach, the total score is 0 regardless of scores 2-6.
1.
2.
3.
4.
5.
6.
Pool Description
Are there any pools in the reach?
Are there both lateral and mid-channel pools in the reach?
Is the reach channelized?
Is there any cover marked in the pools?
Are there any pools >70 cm deep?
IF YES to #5, are there any pools <70cm deep? (score = 0
if #5 = 0)
50
Score
Yes
No
1
0
1
0
0
1
1
0
1
0
1
0
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
159
Based on a sum of scores:
One point is given for each criteria met, range 0-4. If there are no pools in
the reach, the total score is 0 regardless of scores 2-4.
Pool score
1.
2.
3.
4.
160
161
162
163
164
Max of pool max
Deepest fines in pools
Average of fines in pools
Average substrate size in pools
Proportion of cover in pools
Pool Description
Are there any pools in the reach?
Are there both lateral and mid-channel pools in the reach?
Are there any pools >70 cm deep?
IF YES to #5, are there any pools <70cm deep? (score = 0
if #5 = 0)
Score
Yes
No
1
0
1
0
1
0
1
0
Deepest pool depth across the reach
Deepest measurement of fines in all pools across the reach
Average of depth of fines in all pools across the reach
Dominant and sub dominant substrate sizes averaged (see number 49 for sizes)
Sum of all cover scores across all pools divided by (number of pools*9)
Other units
165
166
167
168
169
170
171
Number of runs
Number of transitional units
Proportion of runs
Proportion of transitional units
Number of unit types
Most common unit
Reach unit types match
172
173
174
175
Total number of units
Predominant channel type
Max of max depth unit
Unit variance
Number of runs in the reach
Number of transitional areas in the reach
Proportion of units that are runs in the reach
Proportion of units that are transitional units
Number of unit types in a reach (range 1-4)
The unit type that occurs most often in the reach, if it's a tie, the cell is blank
Does the most often unit type match what was selected as predominant for the reach
(0,1)
Total number of units in each reach
Collected at the reach scale (pool, riffle, or run)
Deepest max depth across all the units
Sum (number of units + number unit types)
Thalweg
176
177
178
179
180
181
182
183
184
185
Thalweg min
Thalweg max
Thalweg mean
Thalweg max : min
Thalweg mean : max
Thalweg range
Thalweg variance
Variance of max depth unit
Run max variance
Run max mean
Smallest of the thalweg depths across the reach
Largest of the thalweg depths across the reach
Mean of the thalweg depths across the reach
Ratio of the largest to the smallest depths (max depth divided by min depth)
The average thalweg depth divided by the max thalweg depth
The max thalweg depth minus the min thalweg depth
Variance calculated using the 10 thalweg depths
Variance calculated using the max depth of all units across the reach
Variance of the max depths across the runs in each reach
Mean of the max depths across the runs in each reach
Flow
186
187
188
Predominant flow reach
Predominant flow units
Flow reach units match
Collected at the reach scale (no detectable, slow, moderate, fast)
The type of flow most commonly chosen in the units, if it's a tie, cell is blank
Comparison of "predominant flow reach" with "predominant flow units" (yes/no)
51
Appendix A cont. A list of all candidate metrics examined.
ID Candidate Metric
Description of the metric
189
190
191
192
193
194
195
196
197
198
199
Proportion of no flow units
Proportion of slow flow units
Proportion of moderate flow units
Proportion of fast flow units
Number of flow types
Proportion of slow-no flow
Proportion of moderate-fast flow
Proportion of slow flow
Proportion of fast flow
Slow : fast
Mean velocity
200
201
Current QHEI
Hydro diversity
Proportion of units marked as "no detectable" flow
Proportion of units marked as "slow" flow
Proportion of units marked as "moderate" flow
Proportion of units marked as "fast" flow
Number of flow types in a reach (number 1-4)
Number of units marked as slow or no flow divided by total number units
Number of units as moderate or fast flow divided by total number units
Number of units marked as slow flow divided by total number units
Number of units as fast flow divided by total number units
Proportion of slow flow divided by Proportion of fast flow
An average of the flows across units (no detectable = 0, slow = 1, moderate = 2, fast
= 3)
Sum (Thalweg max + Count flow types)
Sum (Count of channel unit types + Count of flow types)
52
Appendix B. Example field sheets including information collected at each site.
53
Appendix B cont. Example field sheets including information collected at each site.
54
Appendix C. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
55
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
56
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
57
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
58
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
59
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
60
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
61
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
62
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
63
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
64
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
65
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
66
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
67
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
68
Appendix C cont. Statewide and Regional Scoring Plots for the Illinois Habitat Index.
69
Appendix D. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat Index.
Procedure for Physical Habitat Measurements
and Scoring of the Illinois Habitat Index
Introduction
This document provides a summary of the methods needed to conduct a general
evaluation to score the Illinois Habitat Index (IHI). The included site evaluation form at
the end of this document is to be used to collect the field data needed to calculate the IHI
score. The following protocol should be used to complete the site evaluation form.
General information
Stream: The official name of the stream may be found in the Illinois Atlas & Gazetteer
(DeLorme 2003) or in ESRI ArcMap data layer (NHD Streams). If these two sources do
not match, list both names for the stream on the data sheet.
IEPA Station Code: At many sites, official Illinois Environmental Protection Agency
(IEPA) station codes have been assigned. If no stream code has been assigned, one can
be requested from the IEPA by providing GPS coordinates, stream name, and text
description of the location.
Scorer: If the forms have not been previously filled out by the scorer, include their full
name and contact info in the comments section.
Location Information: Accurate location information is essential. Always enter an exact,
very descriptive location on every scorer’s datasheet including the name of the county,
the gazetteer page number and coordinates, the road that crosses the stream, the closest
city in the gazetteer, and the direction from that city. This information is especially
important when the stream code is unknown. This will prevent any “orphans” at the end
of the season.
Fill out the site and location information for all sites visited. If a site is not sampled,
explain in the comments why it was not sampled (e.g., “stream is flooded, will visit later”
or “stream is too large, no subsequent visit is necessary”).
Latitude/Longitude: Set your GPS to record in NAD83, Lambert. GPS and all location
information should be written on the datasheet in addition to the IEPA code.
70
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
Reach Characteristics
The access point to the sample reach will most often be a road crossing; the assessment
should be made while walking upstream from the road crossing (access point) unless
something prevents upstream assessment or it is known that coordinated sampling is
conducted downstream of the access point. Assessment should not include effects of the
road crossing on the physical habitat of the stream reach. Scorers should walk upstream
from the bridge until bridge effects are not apparent (rarely more than 30 m) to start the
sampling reach. If no apparent differences are seen, the sample reach should be started
10 m upstream of the access point. Record the distance from the access point at which
the sample reach starts and circle whether this is upstream or downstream. Take all
measurements in 1/10 m (e.g., 1.5 m) except depth, which should be measured to the
1/100 m (e.g., 0.86 m).
A representative stream reach is determined by sampling a reach length of 20 times the
average wetted width. A minimum of 100 m and a maximum of 300 m should be
surveyed to evaluate stream characteristics and habitat quality. Total reach length is
determined by measuring the wetted width at the beginning of the sample (i.e., 10 m
upstream of the bridge) then walking upstream 10 x that distance, at which point the
middle wetted width is taken. Scorers should walk 10 x the middle wetted width and
then to the end of the current channel unit to obtain the total reach length. If no end to
the channel unit is in sight (e.g., the reach is a channelized ditch), total reach length is
ended at 20 x the average wetted width. Don’t forget to measure the thalweg depth at the
downstream, middle and upstream points as well. Thalweg is defined as the deepest
depth in the stream cross-section. Width and thalweg measurements should be taken in
areas that appear representative to the stream reach. (i.e., avoid areas that are extra wide
or extra narrow compared to the rest of the reach).
Collecting information to score metrics
The Illinois Habitat Index (IHI) is designed to provide a qualitative evaluation of the
general characteristics of physical habitat and response to human degradation in the
upstream and local watershed. The IHI is composed of five metrics, and each are
described herein. Each metric is scored and then all five are summed for the total IHI
score. The maximum possible score is 24; the score increases with better quality habitat.
Methods for data collection are described, how to score each metric, and how to combine
them for the final IHI score. Standardized collection of the data is essential for assigning
an accurate IHI score. Scores are encouraged to consult each other to ensure similar
scoring approaches.
71
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
Metric 1: Buffer_bare
This metric is the sum of the Average Buffer code and Bare: the average measure for
the amount of bare soil visible on the stream banks. The metric value can range from 09.
Buffer width is the area adjacent to a stream that is not developed or disturbed (i.e.,
without human perturbation). A coarsely mowed buffer between an agricultural field
(but not a field road) and a stream is ok, but a manicured lawn is not a buffer. Mark only
one box with an X for each bank (Left and right, looking upstream). The two boxes
checked are given a code and the two measures are averaged for Average Buffer. Bare
Stream Bank is a measure of the amount of bare soil exposed on each stream bank. The
two boxes checked on the Habitat Evaluation Form are given a score and the two scores
are averaged for the measure of Bare.
Buffer measure
Very Wide >
100m
Wide 50-100m
Moderate 10-50m
Narrow 5-10m
Very narrow 15m
None <1m
Code
5
Bank
measure
None
Sparse
Intermediate
Abundant
4
3
2
1
Measure
0
1
2
3
0
BB = [(Buffer L + Buffer R)/2] - [(Bank L + Bank R)/2] +3
Metric 2: Substrate Ratio
This metric is the natural log of the ratio of the larger of the two substrate codes to the
smaller plus one.
Substrate in Reach denotes the primary and secondary dominant substrates for each
reach. Substrate types and size categories that were used are defined in the IEPA Quality
Assurance and Field Methods Manual, Section E (IEPA 1994).
Substrate Size Categories:
Substrate
Particle size
Bedrock
Solid rock, large flat slabs of rock not separate from the bottom of
the stream
Silt
<0.062 mm
Sand
0.062-2 mm
Fine Gravel 2-8 mm
Gravel
8-64 mm
Cobble
64-256 mm
72
Code
10
1
4
5
6
7
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
Boulder
Slab
Boulder
Clay
Hardpan
>256 mm
Relatively flat with longest measurement >256 mm
9
8
Material that adheres to itself when squished through your fingers
Soil that is compacted to a hardened impermeable layer; it often
feels slick and is associated with streams that have clay in them.
3
3
SR =ln ([larger dominate substrate code/smaller dominate substrate code] + 1)
Metric 3: Percent Shade
This metric describes the amount of shading the water in the stream receives during the
hours between 10 a.m. and 2 p.m. Scorers should check the appropriate box, and then
assign the percent shade to the metric based on the table below.
Description
Percent Shade
(PS)
Water surface completely shaded
Water mostly shaded with some sunlight
Half water surface shaded, half full
sunlight
Most water surface receiving sunlight
Lack of canopy; full sunlight reaching
water
100
75
50
25
0
Metric 4: Proportion of Riffles
As the scorer is walking back to the access point, each channel unit should be noted on
the data sheet as a riffle or other. Proportion of riffles is calculated by dividing the
number of riffles in the reach by the total number of channel units.
PR = (number of riffle units/number of total units)
Metric 5: Proportion of Large Woody Debris
Amount of large woody debris and aggregate wood in each unit should be indicated for
each channel unit as none (0), sparse (1), intermediate (2), or abundant (3).
Proportion of large woody debris is calculated using only the channel units marked as
“other”. The scores of large woody debris and aggregate woody debris are summed
(range for the reach is {[0-6]*# of non-riffle units}). The metric value is calculated as:
LWD = ln ([sum of scores for non-riffle units ]/[number of non-riffle units*6]+1)
73
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
Scoring the IHI
The IHI Score is the sum of the metric scores for the five metrics. Metrics are scored
using x-y graphs specific to each ecoregion. For sites in Illinois that are not located in an
area with ecoregion specific graphs the Statewide scoring graphs should be used. To
score each metric, locate the x-y graph for that metric in that ecoregion (Appendix C).
Plot the metric measure against the appropriate covariate (value labeling the x-axis).
Your metric is given the score coordinating to the area in which the point falls. Score all
five metrics in this manner and sum the five scores for the IHI score.
IHI = Metric ScoreBB +Metric ScoreSR + Metric ScorePS + Metric ScorePR + Metric
ScoreLWD
EQUIPTMENT LIST
1. Map of Site Location
2. GPS (NAD83 Lammert Datum)
3. Camera
4. Extra batteries
5. Pencils
6. Habitat Evaluation Forms (printed on rite-in-the-rain paper)
7. Measure Tape (preferably in meters)
8. Depth rods (meter sticks or PVC pipes with depths marked every 1/100 m work well)
9. Waders/water shoes
10. Sun screen
11. First Aid Kit
12. Bug spray
74
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
Acknowledgements
We would like to acknowledge all the of the people who have helped us with their
valuable time and input for this project including the IDNR streams biologists, IEPA, and
the summer field staff especially Steve Warrner, Jeff Fore, Jeff Butler. Special thanks to
Roy Smogor, Brian Metzke, Leslie Bol, and Robert (Bud) Fischer. This workbook is
based largely on work done by Laura Sass and Leon Hinz of the Natural History Survey
and Ann Marie Holtrop of the IDNR. Funding was provided to the Illinois Natural
History Survey through Illinois’ State Wildlife Grant Program (T-25-P-001).
75
Appendix D cont. Procedure for Physical Habitat Measurements and Scoring of the Illinois Habitat
Index
HABITAT EVALUATION FORM
Location Information
County
Gaz pg and coord.
Latitude
Longitude
Road crossing
Nearest town
Direction
N NE E SE S SW W NW
Stream:
Date:
IEPA
Station Code:
Scorer(s):
Page __1__ of _____
Notes:
REACH CHARACTERISTICS
Check one box per bank. River right looking upstream.
Buffer Width
Bare Stream Bank
L
R (Per Bank)
Very Wide > 100m
Wide 50-100m
Moderate 10-50m
Narrow 5-10m
Very narrow 1-5m
L
Wetted Width Thalweg Depth
Downstream
Middle
Upstream
Average
R (Per Bank)
None
Sparse
Intermediate
Abundant
None <1m
Reach Length______________m
Substrate in Reach
Shading of Water Surface
M ark do minant and next do minant substrates
M ark a to tal fo r the reach
Boulder (>256 mm)
Slab Boulder (>256 mm)
Cobble (64-256 mm)
Gravel (8-64mm)
Fine Gravel (2-8 mm)
Sand
Clay/Hardpan
Silt
Water surface completely shaded
Water mostly shaded with some sunlight
Half water surface shaded, half full sunlight
Most water surface receiving sunlight
Lack of canopy; full sunlight reaching water
Number of channel units ________
Reach starts ____m from bridge.
Sampling from bridge is
UPSTREAM
DOWNSTREAM
Bedrock
CHANNEL UNIT CHARACTERISTICS
Circle Type:
m
m
m
m
Circle Amount: (0=None, 1=Sparse, 2=Intermediate, 3=Abundant)
1 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
2 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
3 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
4 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
5 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
6 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
7 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
8 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
9 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
10 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
11 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
12 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
13 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
14 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
15 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
16 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
17 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
18 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
19 Riffle
Other
0 1 2 3 Large Woody Debris
0 1 2 3 Aggregate Woody Debris
76
m
m
m
m