The paper presents the results of an investigation of physical-chemical features of water as well as rotifer and crustacean abundance and diversity measures, relating to the taxonomic richness and species diversity index, in three lobelia lakes differing in trophic status and morphometric features. The main purpose of this study was to establish the diversity of zooplankton communities in the open water area of lobelia lakes, including extracting species common for each lake and also to find environmental predictors which are responsible for the development of zooplankton communities. Despite the fact that the three studied lakes are of the same origin, located in the same vicinity and have generally similar environmental factors, zooplankton community structure revealed a great variation in reference to species diversity (only ca. 20% of the species were common for all lakes) and particularly in inhabiting species. Obrowo Lake had the most diverse assemblages of both rotifers and crustaceans compared to Modre and Pomysko lakes. In the taxonomic structure species that are rare for the Polish fauna, such as e.g. Holopedium gibberum and Heterocope appendiculata, occurred. Even though the examined lobelia lakes are ecosystems that undergo varying human-induced impacts, they still remain taxonomically very variable aquatic ecosystems, containing rare species of very high ecological status. The observed symptoms of deterioration of water quality, reflected in the zooplankton biocoenotic features, showed that the best conditions were attributed to Obrowo Lake in comparison with the two remaining lakes – Modre and Pomysko. Total nitrogen and chlorophyll a concentration were decisive for the distribution of zooplankton species in Pomysko and Obrowo lakes, while in case of Modre lake water reactivity and conductivity were of higher impact.