The structure and dynamics of plankton communities in the coastal zone of the Curonian Lagoon of the Baltic Sea in January-December 2017–2021 was studied. It was found that at the coastal shallow littoral station surrounded by macrophytes the species diversity was higher, and the quantitative characteristics of phytoplankton and zooplankton were lower in all seasons and years of the study than at the deeper coastal station located behind the macrophyte belt. The exception was the period when, as a result of surge events, the phytoplankton biomass in the coastal littoral in October–November 2018 increased to 326–627 g/m3. Every year, “blooms” of water by Cyanobacteria with different intensity and duration were observed at the Lagoon. The abundant of cells of potentially toxic Сyanobacteria exceeded the World Health Organization standard, as a rule, in the summer months at a deep-water coastal station, especially in 2017–2018. This had a negative impact on the state of the entire ecosystem, primarily on zooplankton organisms, in which communities the proportion of dead individuals increased. Water during the period of Cyanobacterial “blooms” in summer and autumn 2017–2018 also had an acute toxic effect on planktonic test organisms.