The species composition, abundance and biomass, trophic relationships of phytoplankton and zooplankton, as well as the proportion of dead individuals in zooplankton were studied in the water system "Pregolya River – Kaliningrad Sea Channel (KSC) – Vistula Lagoon – Baltic Sea" in July, August and October 2021. In total 173 taxa of phytoplankton and 73 taxa of zooplankton were found during period of investigation. The maximal species diversity was observed in the summer period, in autumn it was decreasing. The maximum number of taxa for both phyto- and zooplankton was found in the Vistula Lagoon and in the KSC, the minimum – in the Baltic Sea. In summer the 3 communities in phytoplankton, 4 in zooplankton, in autumn – 3 communities in both phyto- and zooplankton were found. The plankton communities were confined to water areas with different salinity: The Pregolya River, the KSC and the Vistula Lagoon, the Baltic Sea. The dominant complex of species at the stations differed; species of a predominantly freshwater complex were noted in the Pregolya River, brackish-water species were found in the Vistula Lagoon, and a marine complex of species was identified at the stations of the sea strait and in the Baltic Sea. More abundant plankton communities both in summer and autumn were in the KSC and the Vistula Lagoon (phytoplankton biomass varied from 1.19 g/m3 to 11.89 g/m3; zooplankton biomass varied from 305 mg/m3 to 1801 mg/m3). In this area the most optimal conditions for the development of plankton were formed such as an increased nutrient content and maximum water heating. Plankton communities both in the Pregolya River and in the Baltic Sea in summer and autumn were less abundant (phytoplankton biomass varied from 0.16 g/m3 to 2.50 g/m3; zooplankton biomass varied from 34 mg/m3 to 468 mg/m3). The most intense trophic relationships in the plankton community in the summer in the Baltic Sea, optimal – in the KSC and in the Vistula Lagoon were formed. The proportion of dead individuals in the zooplankton of the studied system in both seasons was maximal in the areas, which had the critical salinity for hydrobionts and high turbulence conditions such as KSC, the Sea strait and at the exit from Sea strait.