In a warming future climate, the sea ice cover is expected to decrease, with very likely large consequences for the marine ecosystem. We investigated the impact of future sea ice retreat on the Baltic Sea biogeochemistry at the end of the century, using an ensemble of regionalized global climate simulations. We found that the spring bloom will start by up to one month earlier and winds and wave-induced resuspension will increase, causing an increased transport of nutrients from the productive coastal zone into the deeper areas. The internal nutrient fluxes do not necessarily increase because they also depend on oxygen and temperature conditions of the bottom water. Winter mixing increases in areas having reduced ice cover and in areas having reduced stratification due to increased freshwater supply. The reduced sea ice cover therefore partly counteracts eutrophication because increased vertical mixing improves oxygen conditions in lower layers.