The current state and changes in biological communities of the Russian part of the South-Eastern Baltic Sea during two first decades of twenty-first century is considered. In phytoplankton, some typical cold-water dominants have been lost from the spring complex of species and the productivity of summer phytoplankton has been 4–7 times higher in some years. The species composition and spatial distribution of zooplankton in the shallow water zone are analyzed. For the first time, distribution patterns for macroalgae communities are determined for the Russian South-Eastern Baltic Sea, including biotopes dominated by perennial red alga Furcellaria lumbricalis. It is shown that the maximum depth of macroalgae growth in the study area has shifted toward lower depths in comparison with those characteristics of the Baltic Sea. The location, composition, and structure of bottom macrozoobenthos communities are described. For the first time for the study area, lists of species of phytoplankton, zooplankton, and phytobenthos are presented. The revised list of macrozoobenthos species is also provided.