The past of the Baltic Sea has been intensively investigated using a wealth of techniques. By far the largest number of studies has focused on sea level and salinity changes, driven by global climate and isostatic crustal rebound after the Baltic Sea emerged underneath the Weichselian Ice Sheet ca. 15,000 cal. years BP. The post-glacial history of the Baltic has included both freshwater and brackish water stages depending on the connection of the Baltic Sea with the world’s oceans. As the Baltic is one of the most polluted sea areas in the world, many studies have also focused on both the long-term trends in nutrients and productivity and the relatively recent anthropogenic eutrophication. The long-term changes in the trophic state of the Baltic Sea have been found to be linked to changes in climate, which controls freshwater discharge from the catchment and weathering rates, as well as marine water inflow from the North Sea. The productivity of the Baltic Sea has followed major climate patterns: it was high during warm periods and lower during phases of deteriorating climate. Recent eutrophication of the Baltic Sea can mainly be explained by a marked increase in discharge of nutrients caused by a growing population and changes in the agricultural practice, although long-term climate variability also plays a part. Signs of recovery have recently been detected, however, the Baltic Sea is still far from its pre-industrial trophic state.