Zooplankton was investigated in three small lakes (Chetyryohverstnoe, Lamba and Karjer) of Lake Onega drainage basin, which are situated within the City of Petrozavodsk and exposed to human impact. The species composition, abundance and biomass were determined for the spring, summer and autumn-winter seasons. Sixty-one Crustacea and Rotifera species belonging to different ecological groups (pelagic, littoral-thicket, bottom and eurybionts) were identified. Seasonal changes in the structure of zooplankton communities were demonstrated. The species diversity and quantity were the highest in August. The pollution rate of the lakes was assessed based on the indicator-species composition. It was determined that the water in lakes Chetyryohverstnoe (S = 1.42) and Lamba (S = 1.45) belonged to the oligosaprobic type and class II of water purity, while Lake Karjer (S = 1.58) fell into the betamesosaprobic type and class III.