Changes in phytoplankton communities due to anthropogenic nutrient load and climate change often lead to eutrophication and harmful algal blooms that can affect biogeochemical cycling. However, little is known about the specific responses of various species to environmental variables. 17-year long data on the midsummer phytoplankton biomass in the Neva Estuary were analyzed to show the changes in the composition of phytoplankton in relation to water depth, transparence, salinity, temperature, concentrations of total phosphorus and chlorophyll a, and plankton primary production. One hundred seventy-four species and forms from eight taxonomic classes were found in phytoplankton. Fifteen species were potentially harmful. The most diverse and abundant groups were cyanobacteria, green algae and diatoms. Canonical Correspondence Analysis showed that the biomass of various species from each phytoplankton group correlated differently with environmental factors. However, within each group, there were some predominant trends in the correlative response to changes in environmental variables. The biomass of cyanobacteria was high in the middle and lower reaches of the estuary and, in general, positively correlated with water salinity. The biomass of most species of green algae and diatoms correlated negatively with it. These algae showed a positive trend in biomass in the upper and middle reaches of the estuary during the last decades that may be explained by changes in weather conditions. Taking into account that climate models predict future increases in precipitation and temperature in the northern Baltic, the future expansion of freshwater phytoplankton species in estuaries of the northern Baltic Sea is very likely.