Marine heatwaves (MHW) are globally occurring events observed with potentially long-lasting ecological effects and socio-economic repercussions. The Western Baltic Sea (WBS) is a transitional region between the North Sea and the Baltic Proper characterized by a unique physical oceanography. Warming of the area in response to climate change is significant, but the temporal and spatial development of extreme temperature events is poorly understood and documented. Here, we analyzed retrospective runs performed by a 3D-hydrodynamic model over seven decades (1950-2022) to better understand MHWs in the WBS. Our analysis revealed rampant increases in extreme temperature events since the 1990s. MHWs occurred regularly in spring and summer, but increasingly as well in autumn and winter. We especially identified long-lasting extreme events at the surface (> 100 days) and at the bottom (> 400 days) that resembled the exceptional “Blob” phenomenon in the Pacific Ocean. We furthermore identified parts of the WBS that in addition to extreme temperatures suffered hypoxic conditions, a combination of pressures with potentially devastating ecological impacts. Our study advances the understanding of the climatic impact on a marine system that already suffers from eutrophication and overfishing, and provides baseline knowledge to understand physical forcing impacts on ecosystem functioning.