The study concerns the relationships between taxonomic, functional and phylogenetic diversity of benthic invertebrates inhabiting watercourses and abiotic parameters associated with excessive nutrients load (concentration of Kjejdahl nitrogen, nitrates, phosphorus, organic carbon and dissolved oxygen, values of BOD5 and electrolytic conductivity). The research used data on the species composition of leeches, molluscs and larval forms of odonates and chironomid dipterans. Their description using mathematical functions allowed to determine whether the diversity reaches maximal values at extreme or moderate values of nutrients enrichment. In most cases, statistically significant relationships were unimodal—the highest diversity was observed at intermediate values of nutrients content and associated parameters, however the different patterns of relationships, monotonic and inverse quadratic, were also observed. Indirect impacts of nutrients enrichment on diversity were found as the most significant relationships. Significant responses of functional diversity were clearer and stronger than responses of taxonomic and phylogenetic diversity. The identification of fauna to the species level allowed for obtaining precise results that could enable selection of appropriate parameters for effective assessment of environmental degradation.