Anthropogenically elevated nutrient concentration occurs in both ground and surface waters and cause grave environmental problems which are responsible for the degradation of water quality on a worldwide scale. The progressive anthropogenic pressure caused by prolonged agricultural activity has a negative effect on most water ecosystems including rivers and reservoirs. Freshwater molluscs, which are hololimnic organisms, have a limited mobility; therefore, they are good bioindicators of changes in their habitats. They reflect the abiotic or biotic state of water habitats, which represents the impact of environmental change on the habitat, community as well as on the ecosystem. A long-term survey of mollusc communities revealed the occurrence of 44 species including some rare, vulnerable, threatened or legally protected species, e.g. Borysthenia naticina, Unio crassus, Anodonta cygnea, Pseudanodonta complanata or Sphaerium rivicola, in the Wkra River, its tributaries and selected oxbow lakes. In the Wkra River catchment area, the mollusc communities, including U. crassus (Habitats Directive Natura 2000), are under a combined effect of several environmental factors. Conductivity, hardness, current velocity, river width, temperature, nutrient concentration and the size of sediment particles were the parameters most associated (statistically significant according to the forward selection results) with the distribution of mollusc species. The forward selection results showed that the concentration of dissolved oxygen and the occurrence of macrophytes also exerted a significant influence on the distribution of Mollusca. Among environmental factors, anthropogenically elevated concentrations of nitrites and nitrates in the water were the most predictive parameters that negatively influenced (stressors) the structure of mollusc communities. The novel findings of this survey showed that some mollusc species could tolerate wider ranges of some environmental factors and higher concentrations of nutrients than had been expected. U. crassus is more tolerant of a relatively high concentration of nitrates in the water than was previously expected, as well as of nitrites and phosphates, and it can survive in rivers with relatively high nutrient concentration. The present results confirm both the field and the toxicological research on the negative effect of nitrites and nitrates, which is caused by their toxicity to freshwater molluscs. The number of individuals, number of mollusc species and density decreased dramatically within the last year of the survey in the Wkra River and its tributaries. This phenomenon seems to be a direct result of the nutrient enrichment in the Wkra River catchment area, the regulation of riverbeds or an indirect result, e.g. lack of primary or appropriate host fishes for unionid species. The declining trend in the global mollusc population has probably begun to occur in the Wkra River catchment area.