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Ciliates constitute an important trophic link in aquatic environments, because they are essential food sources for zooplankton and fish. In this study, the spatial differences in abundance and composition of ciliate communities in relation to varying water salinity were investigated. The study was conducted in the large, brackish, eutrophic lakes Gardno and Łebsko. In the studied lakes, no significant differences among ciliate communities were identified among sampling sites. Ciliate communities in Lake Łebsko were characterized by a high contribution of tintinnids, with mean values at particular sites between 32% and 36%. In Lake Gardno, where salinity was lower, the importance of tintinnid ciliates increased after a marine water intrusion into the lake. In both lakes, the importance of tintinnids in ciliate communities was higher than in adjacent fresh and marine waters. Shortly after wind-driven intrusions of marine waters (backwaters), the marine and brackish mixotrophic ciliate Mesodinium rubrum was observed in both lakes. Once, in the eastern part of Lake Łebsko, Mesodinium major (= Mesodinium rubrum forma major) was observed after a strong backwater when salinity reached 5.4 PSU.