Periphytic rotifer assemblages from lentic habitats are understudied. To improve knowledge on the principal environmental determinants of their structure and composition, we examined summer periphyton from 184 freshwater bodies from a taxonomic and multi-trait-based perspective. Only the latter allowed consideration of all bdelloids. Alpha diversity decreased with electrolyte and aluminium concentration but increased with macrophyte richness, pointing at salinization, metal toxicity and loss of structural niche heterogeneity as potential threats for rotifer diversity. Replacement was the prominent component of beta diversity, with acidified sites showing the highest local contributions. Variation partitioning indicated that local conditions explained variation in species composition best, but general setting (soil type, land cover, connectivity) and spatial context were also not insignificant. Redundancy analysis related species composition more particularly to gradients of pH and trophic status, whereas the representation of functional groups was structured mainly by phytoplankton productivity. Mirroring shifts observed in the plankton, high phytoplankton productivity associated with larger size and more detritibacterivory. Dominance of collectors constrained variation in guild ratios, underlining the need for more refined functional approaches. To aid the use of periphytic rotifers in regional water quality assessment, we identified indicators and community thresholds for pH and trophic variables and determined optima and tolerances for individual taxa.