Multiple stressors, such as overfishing, pollution, climate change, biological invasions etc., are affecting fish communities, and thus can have versatile effects on marine ecosystems and socio-economic activities as well. Understanding the changes in the fish community structure is ecologically and economically important, yet a very complex issue, requiring comprehensive analysis of multiple factors. The role of regional oceanographic variability, namely, coastal upwelling, is often neglected when it comes to the analysis of fish assemblages. In this perspective, we were aiming, for the first time in the Baltic Sea, to assess the upwelling influence on fish communities and fish community-based ecological indices used under Marine Strategy Framework Directive. The study covered a long-term period (2000–2019) for upwelling identified by satellite data analysis and fish gillnet surveys, performed in three distinct locations in the coastal waters of the SE Baltic Sea. Overall, our study revealed that temporal dynamics of fish abundance and community composition were associated with the presence of coastal upwelling. The study outcomes suggest that the fish community was more diverse and a higher number of some fish species was observed before upwelling. During upwelling, there was more evident dominance of 1–2 main marine fish species. Through the changes in fish abundance and species composition upwelling was also responsible for the changes in fish community structure-based indices for marine environment status, i.e., in the majority of the cases a decrease in Trophic, Piscivorous Fish, and Diversity indices were observed. Our study demonstrates that upwelling can affect both, the quantitative and qualitative characteristics of coastal fish communities, therefore, it is important to consider this when predicting shifts in the distribution of fish stocks or assessing environmental status indicators, especially under changing climate. We believe that our approach adds novel information to the study of coastal ecosystems of the Baltic Sea and is important for better management of socio-economic activities in the coastal zone.