Hypoxia is a major environmental threat for coastal seas, including the strongly-stratified Baltic Sea in northern Europe. There, a pronounced increase in nutrient loads since the 1950s led to the development of one of the largest hypoxic areas worldwide. So far, other drives of hypoxia, like the increase in water temperatures due to global warming, have been considered minor compared to eutrophication. We show, by analyzing 159-years long hindcast simulations of three different Baltic Sea models, that exceptional warming trends in deep water layers of the western Baltic Sea deteriorated the local oxygen conditions. The above-average warming is only to a small extent attributed directly to global warming, but mainly to a shift in the seasonality of saltwater inflows from the North Sea towards more warm summer and early autumn inflows. Hence, we identify a so far unknown driver of oxygen depletion in the western Baltic Sea with potentially serious ecological consequences.