Large-scale Euro-Atlantic variability, shaped by the polar jet stream, governs weather and climate in the Baltic Sea region, thereby impacting the physical and biogeochemical properties of the Baltic Sea ecosystem. This review synthesizes how key atmospheric circulation features and modes of climate variability, including the North Atlantic Oscillation, atmospheric blocking and the Atlantic Multidecadal Variability, influence the Baltic Sea region. By integrating evidence from the published literature, observational datasets, and both global and regional climate model simulations, we assess established as well as potential linkages to key climatic variables, including temperature, precipitation, and storm activity, across temporal scales ranging from synoptic events to multidecadal variability. We then evaluate how these climate controls cascade into ecosystem-relevant processes, namely oxygen dynamics, primary productivity and ocean acidification. Although physical links are already established, the pathways connecting large-scale atmospheric patterns to biogeochemistry are still poorly constrained, partly because dedicated field studies and targeted model experiments are limited. We outline priority research needs to enhance near-term predictability and reduce uncertainty in future projections for the Baltic Sea.