Cladocera are one of the most important freshwater biological indicators for a wide range of environmental variables. They show strong responses to several environmental factors (e.g., trophic state, water depth, temperature) and are very sensitive to changes in water pH. The main interest of this study was to evaluate the relationship between subfossil Cladocera community composition and environmental properties of dystrophic lakes (pH, water transparency, conductivity, dissolved oxygen, depth and area). We hypothesize that Cladocera species composition depends on a dystrophication index (HDI); thus, Cladocera assemblages change with the degree of dystrophication. For the study, we selected a group of dystrophic lakes located in Wigry National Park (WNP), NE Poland, where we found subfossil remains of 24 Cladocera species belonging to four families (Chydoridae, Bosminidae, Daphniidae, and Sididae). A non-metric multidimensional scaling (NMDS) was used to elaborate on the similarities among samples in cladoceran-community composition and structure. Statistical analyses showed that Cladocera assemblages in all the studied lakes were similar, and individual Cladocera species respond to the measured environmental parameters (e.g., pH, lake size and depth). Our results suggest that in dystrophic lakes, Cladocera community composition is an emerging characteristic of individual species responses to the environment.