The pelagic plankton system of Lake Onego, in its central part and Bolshoe Onego Bay, has a high structural and dynamic stability. The purpose of this study was to assess
the state of zooplankton in Lake Onego and its seasonal variation in years with different temperature conditions based on data for 2015–2017. The main zooplankton parameters,
its composition, structure, and features of the annual cycle have been preserved over this period, but an elevated spatial-temporal variation was observed, associated with the different thermal regimes in these years. In July 2016, zooplankton development shifted to earlier dates and reached extremely high parameters, atypical of this period (abundance of 6,200 ind./m3 and biomass of 0.21 g/m3). The first decade of August 2015 was noted for low amounts of zooplankton (abundance of 1,200 ind./m3 and biomass of 0.03 g/m3), whereas the same period in 2017 was characterized by its elevated amounts (abundance of 7,500 ind./m3 and biomass of 0.17 g/m3). Zooplankton abundance and biomass in June and October corresponded to their long-term averages, taking into account interannual fluctuations. The detection of extremely deviating minimum and maximum zooplankton abundances may indicate that the lake’s plankton system is beginning to lose balance in the conditions of temperature differences among years.