Kondopoga Bay is one of the largest bays of Lake Onego. For many years (since 1929), the bay has been experiencing significant anthropogenic stress due to operations of the Kondopoga Pulp and Paper Mill (PPM). The PPM had gone through several stages characterized by different volumes and compositions of wastewater. In the 1980s, the influx of nutrients upon the commissioning of a biological wastewater treatment plant triggered anthropogenic eutrophication of the bay. In recent decades, there appeared yet another source of nutrient pollution – trout farms. A number of studies highlight climate warming as a new factor affecting the plankton system of Lake Onego. The dataset for analyzing the state of zooplankton in Kondopoga Bay was formed by netting performed in 2019–2021. Samples were collected during zooplankton development peaks (late July early August) at three stations: in the bay top, in its central part, and in Bolshoe Onego Bay (for reference). The studies show that no major changes have occurred in the plankton communities of Kondopoga Bay compared to their state late in the 20th century. However, there are signs of early-stage destabilization of the bay’s plankton system, such as a new multi-annual maximum in zooplankton abundance in the Kondopoga Bay top, high abundance of the relict crustacean Limnocalanus macrurus (Sars, 1863) in the central part of Kondopoga Bay and in Bolshoe Onego Bay, changes in the ratio of closely related species of the genus Bosmina (Eubosmina) Seligo, 1900 among the dominants.