Ciliate communities in open waters of the meso-eutrophic Neva Estuary (the Baltic Sea) were studied in summer 2010. Abundance and biomass of ciliates were surprisingly low (0.03–1.9 ind ml–1 and 0.04–2.4 × 10–3 μg C ml–1), especially in samples with high detritus content. During this study we detected four ciliate species which are new for the Baltic Sea. Mixotrophic ciliates dominated at the majority of stations (28–67% of overall ciliate numbers). Their contribution was significantly higher in the outfall area and northern part of the Neva Estuary (Resort District), where total density of ciliates was low. Medium-sized ciliates (30–60 μm) were the most diverse and abundant (average contribution 59% of total abundance). The two parts of the estuary, separated from each other by a storm-surge barrier, differed slightly in their community structure (p < 0.05) but did not significantly differ in ciliate numbers and biomass values.