The Mar Menor is a sheltered and hypersaline lagoon, with salinity ranges between 38 and 51 psu. The lagoon is threatened by several pressures and in the last decades detrimental impact on the natural community structure and dynamics have increased. In the watershed, agricultural practices are rapidly evolving from extensive dry crop farming to intensively irrigated crops, with increasing loads of nutrient and pollutants to the lagoon. Hydrological conditions, nutrients and chlorophyll a concentrations were analysed in 1997 and 2002–2003 in a grid of 20 stations in the lagoon. Different time scales, from daily to inter-annual, were considered. In the considered periods, the dissolved inorganic nitrogen (DIN) increased whilst phosphate decreased significantly. These contrasting patterns depended upon the increased agricultural loading for DIN and were due to the implementation of the wastewater works for phosphates. In 1997 and 2002, the highest nitrate concentrations were usually found on the west coast of the lagoon, close to the mouths of the main watercourses. In parallel, the lowest concentrations were detected at the inner coastline along “La Manga” sandy bar and “El Estacio” channel. Based on weekly data, correlations between chlorophyll a concentrations and environmental variables disagreed with traditional eutrophication models. Relationships between chlorophyll a and nutrients were negative, suggesting that in the short term phytoplankton controlled nutrient concentrations. Moreover, nitrate and phosphorous seemed to alternate as limiting factors. The relationships between chlorophyll a became positive when considering time lags and analysed at longer time scales (monthly or seasonal means), thus suggesting a very rapid response of primary producers to nutrient enrichment. A significant correlation between chlorophyll a concentration and fish larvae density was also found at all time scales analysed, suggesting a top-down control of the trophic web.