Many studies related to the influence of eddies on the primary production chain of marine ecosystems have been conducted; however, this effect tends to be regionally specific, especially in coastal dynamic waters. In the Baltic Sea, mesoscale and submesoscale eddies are a ubiquitous feature of water circulation during summer, when diazotrophic cyanobacteria blooms occur in surface waters due to the excess of phosphorus in seawater. Climatic change may increase the frequency and duration of these negative events in the marine ecosystem. We examined the taxonomic composition, abundance, and primary production of phytoplankton in the southeastern Baltic Sea during the occurrence of the packed eddy system at the end of the abnormally warm summer of 2018. Massive cyanobacteria growth was observed in the plume of the eutrophic Vistula Lagoon in the Gulf of Gdansk. The only species diazotrophic Dolichospermum flos-aquae ((Bornet & Flahault) P. Wacklin, L. Hoffmann & Komárek, 2009) vegetated along the western coast of the Sambia Peninsula. Its colonies reached the highest biomass nearby the dumping site of the Amber Mining Plant in Yantarny, Kaliningrad Region, Russia. The cyanobacteria colonies dispersed in the outgoing jet of a relatively warm eddy dipole. Chrysochromulina spp. (Lackey, 1939) was dominant in these nitrogen-rich waters. In contrast, cryptophyte species dominated in the relatively cold waters of the dipole anticyclone that resulted in a fourfold decline in primary production. The decrease in the number of mobile phytoplankton species was revealed within the “old” eddies near the northern coast of the Sambia Peninsula and the Curonian Spit. Meanwhile, species of the spring–autumn complex Coscinodiscus granii (Gough, 1905), Peridiniella catenate ((Levander) Balech, 1977) and other developed in the community. This implies that the appearance of eddies can cause phytoplankton succession in the coastal area. The mechanism of their influence was similar to the action of other physical factors perturbing a relatively stationary environment. Capture of cyanobacterial colonies by eddies led to an improvement of the ecological situation in the area, as cyanobacteria transported their biomass outside the coastal area. However, the opposite direction processes obviously were the deterioration of light conditions, increased water turbidity, and organic matter concentration.