The aim: complex study of the Baltic Sea ecosystem, including the habitat conditions of aquatic biological resources based on the results of joint research by AtlantNIRO and the P.P. Shirshov Institute of Oceanology RAS (Atlantic Branch). Methods used: analysis of long-term data of joint expeditionary research in the open part and coastal zone of the Baltic Sea.Results: owing to the interaction of AtlantNIRO with AB IO RAS in 2018–2022, the continuity of long-term observations has been preserved and the volume of scientific information necessary for assessing the state of the habitat of aquatic biological resources in the Russian sectors of the Baltic Sea has been increased. Modern data on eutrophication and pollution, on distribution of phytoplankton, zooplankton, benthos, as well as the early ontogenetic stages of the main commercial fish have been obtained. The spatial distribution of plankton and benthic communities, including areas favorable for spawning and feeding of fish, has been detailed. A rather high contamination of bottom sediments with radionuclides in certain areas of the Baltic Sea, primarily in the Gulf of Finland, has been found.Practical significance: the implementation of the areas provided by the Agreement between Rosrybolovstvo and RAS, and above all, the participation of AtlantNIRO scientific groups in expeditions in the Baltic Sea in 2018–2022, was a significant addition to the annual research and state monitoring of aquatic biological resources and their habitats conducted by VNIRO in the Baltic Sea.