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In the Baltic Sea hypoxia has been increased considerably since the first oxygen measurements became available in 1898. In 2016 the annual maximum extent of hypoxia covered an area of the sea bottom of about 70,000km(2), comparable with the size of Ireland, whereas 150years ago hypoxia was presumably not existent or at least very small. The general view is that the increase in hypoxia was caused by eutrophication due to anthropogenic riverborne nutrient loads. However, the role of changing climate, e.g. warming, is less clear. In this study, different causes of expanding hypoxia were investigated. A reconstruction of the changing Baltic Sea ecosystem during the period 1850-2008 was performed using a coupled physical-biogeochemical ocean circulation model. To disentangle the drivers of eutrophication and hypoxia a series of sensitivity experiments was carried out. We found that the decadal to centennial changes in eutrophication and hypoxia were mainly caused by changing riverborne nutrient loads and atmospheric deposition. The impacts of other drivers like observed warming and eustatic sea level rise were comparatively smaller but still important depending on the selected ecosystem indicator. Further, (1) fictively combined changes in air temperature, cloudiness and mixed layer depth chosen from 1904, (2) exaggerated increases in nutrient concentrations in the North Sea and (3) high-end scenarios of future sea level rise may have an important impact. However, during the past 150years hypoxia would not have been developed if nutrient conditions had remained at pristine levels.