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Abstract Similarly to other animal communities, the diversity of subterranean aquatic fauna is influenced by several factors and processes, such as habitat fragmentation, dispersion, environmental heterogeneity, and physical and chemical water characteristics. Here, we studied cave aquatic communities of the Alto Ribeira hydrographic basin, regarding troglobitic and non-troglobitic species, located in a single karst area to evaluate the influence of sub-basins in fauna differentiation. We investigated how abiotic variables (flow, electrical conductivity, temperature, pH, and substrate) influence the fauna composition and the contribution of beta diversity components (nestedness and turnover) in explaining communities’ dissimilarities. Fauna composition differed between sub-basins, as most species did not co-occur in different caves. Caves with higher flow and substrate diversity were the richest. In addition, each cave community was influenced by a unique set of abiotic variables. Dissimilarity among caves was mainly explained by turnover, and our findings suggest the restricted species distribution could be due to ecological (e.g., limited dispersion capacity, tolerance to abiotic variables), hydrogeological (e.g., dispersion barriers, isolation of sub-basins), and historical (e.g., colonization, paleoclimatic events) factors and processes. Therefore, different elements are responsible for determining the composition of cave aquatic communities in different sub-basins, reflecting the variability within a single karst area. processes fragmentation heterogeneity characteristics Here basin nontroglobitic non subbasins sub basins differentiation flow, (flow conductivity temperature pH nestedness turnover dissimilarities subbasins, basins, cooccur co occur richest addition e.g., eg e g (e.g. capacity variables, , variables) barriers sub-basins) colonization events Therefore e.g. (e.g e.g