Globally, evidence for structural changes in coastal marine ecosystems is increasing. Coastal areas are ecologically and socio-economically important, and under multiple anthropogenic stressors. In this study, changes in the structure of fish assemblages were observed during a ten-year study period (1999–2009) in three coastal areas in the northern Baltic Sea. The assemblages differed from each other in terms of species abundances, but a similar shift towards higher proportions of cyprinid fish and lower proportions of pikeperch (Sander lucioperca) was observed in all study areas. The resulting proportional increase of the small-bodied lower trophic level cyprinids was also reflected as declining mean length of fish and mean trophic level in all three assemblages. Variation in fish abundances was related to environmental factors and catches of commercial fisheries. The results suggest that the observed changes were caused by regional patterns of eutrophication in combination with fishing pressure. The results indicate that in the studied systems similar structural changes occurred simultaneously within a relatively short period of time.