Long-term observations (since 1982), which had been carried out in the Neva River estuary, have shown that in 2011–2016 the general nature of distribution, species composition and abundance of phytoplankton differed from those that were recorded earlier. The greatest changes are noted in the central part close by northern coast of the Neva Bay. With observed eutrophication in the Neva Bay (st. 12) and in the eastern part of the Gulf of Finland (st. 19), different groups of algae dominated in the summer phytoplankton (late July – early August). The main mechanism regulating the species composition of phytoplankton were hydrological conditions observed in different parts of the estuary. Also Shallow water, wind activity, oxygen deficiency and temperature stratification, nutrient supply were favorable conditions for development of chlorococcal green, cryptophyte, euglenic and other algae groups. With a high Shannon index (3.8–4.0) in the Neva Bay, the largest share to the total biomass was given by chlorococcal algae. In the resort area of the Gulf of Finland at the end of July – early August, direct temperature stratification was usually established, with enough nutrients creating conditions for the development of stagnophilic planktonic algae with a predominance of cyanobacteria in the epilimion. Here, more often, were periods of surface “blooms”. For the most eutrophied areas of the Neva Bay and the inner estuary the average structural, functional, and relative indicators of plankton were compared with average values for the entire water area. The main characteristics of phytoplankton: biomass, primary production, chlorophyll concentration and total phosphorus content in the northern zone of the Neva Bay, were 2–3 times higher than the average values on the Gulf. The species composition of algae corresponded to a sufficiently high trophic state. In the resort area of inner estuary of the Gulf of Finland (st. 19), the observed mean values also slightly exceeded the average values for the estuary, but the relative indicators differed little from those calculated for the rest of the water area. The structural and functional characteristics of phytoplankton indicated that during eutrophication in different parts of the estuary, in Summer, conditions wer favorable to promote the development of different groups plankton algae.