The Gulf of Finland belongs to the large bays of the Baltic Sea. The eastern part of the Gulf of Finland is an estuary of the Neva River. The heterogeneity of its water masses is typical for the eastern part of the bay. The main reason of such issue is the significant spatial variability of water salinity. The salinity regime is largely determined by the flow of fresh water from the Neva Bay and the spread of seawater from the western parts of the Gulf of Finland. There is a weakening of the influence of river flow and an increase in the influence of saline waters in the direction from east to west. That is why in the eastern part of the bay the general increase of water salinity appears from east to west. The considerable spatial variability of water salinity in the eastern part of the Gulf of Finland creates conditions for the habitats in the plankton for representatives of three ecological complexes: freshwater, brackish and euryhaline-marine. The distribution features of representatives of the indicated ecological complexes in the water area of the eastern part of the Gulf of Finland are considered in the article.