The Gulf of Finland belongs to the large gulfs of the Baltic Sea. The Eastern part of the Gulf of Finland is an estuary of the Neva River. The climate of the Gulf of Finland region is intermediate between marine and continental. Cyclonic atmosphere circulation prevails over the Gulf of Finland throughout the year. The heterogeneity of water masses in the Eastern part of the Gulf of Finland is closely related to significant spatial variability of salinity and water temperature. Water salinity strongly depends on inflow of fresh water from the Neva River and sea water from the West of the Gulf of Finland. Due to peculiarities of hydrometeorological regime, the temperature and salinity of the Eastern part of the Gulf of Finland experiences sharp short-term variations. At the same time, hydrological regime of the Gulf of Finland manifests long-term fluctuations as part of the Baltic Sea. Changeable weather results in instability of the structure of aquatic organisms community. Study concerns the dynamics of zooplankton biomass in the Eastern part of the Gulf of Finland for 1985-2016 under the long-term changes in air temperature and interannual changes in the Neva River inflow.