Marine ecosystems such as the Baltic Sea are currently under strong atmospheric and anthropogenic pressure. Besides natural and human-induced changes in climate, major anthropogenic drivers such as overfishing and anthropogenic eutrophication are significantly affecting ecosystem structure and function. Recently, studies demonstrated the existence of alternative stable states in various terrestrial and aquatic ecosystems. These so-called ecosystem regime shifts have been explained mainly as a result of multiple causes, e.g. climatic regime shifts, overexploitation or a combination of both. The occurrence of ecosystem regime shifts has important management implications, as they can cause significant losses of ecological and economic resources. Because of hysteresis in ecosystem responses, restoring regimes considered as favourable may require drastic and expensive management actions. Also the Baltic Sea, the largest brackish water body in the world ocean, and its ecosystems are strongly affected by atmospheric and anthropogenic drivers. Here, we present results of an analysis of the state and development of the Central Baltic Sea ecosystem integrating hydroclimatic, nutrient, phyto- and zooplankton as well as fisheries data. Our analyses of 52 biotic and abiotic variables using multivariate statistics demonstrated a major reorganization of the ecosystem and identified two stable states between 1974 and 2005, separated by a transition period in 1988–1993. We show the change in Baltic ecosystem structure to have the characteristics of a discontinuous regime shift, initiated by climate-induced changes in the abiotic environment and stabilized by fisheries-induced feedback loops in the food web. Our results indicate the importance of maintaining the resilience of an ecosystem to atmospherically induced environmental change by reducing the anthropogenic impact.