Changes to runoff due to climate change may influence management of nutrient loading to the sea. Assuming unchanged river nutrient concentrations, we evaluate the effects of changing runoff on commitments to nutrient reductions under the Baltic Sea Action Plan. For several countries, climate projections point to large variability in load changes in relation to reduction targets. These changes either increase loads, making the target more difficult to reach, or decrease them, leading instead to a full achievement of the target. The impact of variability in climate projections varies with the size of the reduction target and is larger for countries with more limited commitments. In the end, a number of focused actions are needed to manage the effects of climate change on nutrient loads: reducing uncertainty in climate projections, deciding on frameworks to identify best performing models with respect to land surface hydrology, and increasing efforts at sustained monitoring of water flow changes.