Phytoplankton community structure was studied from 2002 to 2016 in the Vistula Lagoon (southern Baltic Sea) in the context of the 2010 shift in its population, as well as the reason for this shift and its environmental impact. This evident shift was indicated by Multidimensional Scaling at the Bray Curtis similarity level of 31%. Before 2010, the primary components of phytoplankton were Cyanobacteria (up to 98% of the biomass, October 2007) and Chlorophyta (40%, July 2002). After 2010, the contribution of Cyanobacteria considerably decreased, and the proportions of other phyla increased. The total phytoplankton biomass positively correlated with phosphorus, and Cyanobacteria biomass with silica. Evident changes were also observed in the seasonal dynamics of phytoplankton. Before 2010, the highest values of biomass occurred in autumn, and were related to high biomass of Cyanobacteria. Higher biomass has been recently reached in spring, during the dominance of Ochrophyta associated with Chlorophyta, Charophyta, and Cryptophyta. Generalised additive models showed a significant decreasing trend of the total phytoplankton biomass, Cyanobacteria, Chlorophyta, and flagellates, suggesting a decrease in eutrophication. This trend is concurrent with a considerable increase in the ratio of zooplankton to phytoplankton biomass since 2010. The increased ratio, however, did not result from elevated zooplankton biomass, but from the drop in phytoplankton biomass. Therefore, the most probable reason for the decrease in phytoplankton biomass was the simultaneous decrease in the concentration of all nutrients. The potential additional impact of filtration by a new alien bivalve Rangia cuneata G. B. Sowerby I, 1832 is also discussed.