We quantified horizontal transport patterns and the net exchange of nutrients between shallow regions and the open sea in the Baltic proper. A coupled biogeochemical-physical circulation model was used for transient simulations 1961-2100. The model was driven by regional downscaling of the IPCC climate change scenario A1B from two global General Circulation Models in combination with two nutrient load scenarios. Modeled nutrient transports followed mainly the large-scale internal water circulation and showed only small circulation changes in the future projections. The internal nutrient cycling and exchanges between shallow and deeper waters became intensified, and the internal removal of phosphorus became weaker in the warmer future climate. These effects counteracted the impact from nutrient load reductions according to the Baltic Sea Action Plan. The net effect of climate change and nutrient reductions was an increased net import of dissolved inorganic phosphorus to shallow areas in the Baltic proper.