While progress has been made in reducing external nutrient inputs to the Baltic Sea, further actions are needed to meet the goals of the Baltic Sea Action Plan (BSAP), especially for the Baltic Proper, Gulf of Finland, and Gulf of Riga sub-basins. We used the net anthropogenic nitrogen and phosphorus inputs (NANI and NAPI, respectively) nutrient accounting approach to construct three scenarios of reduced NANI-NAPI. Reductions assumed that manure nutrients were redistributed from areas with intense animal production to areas that focus on crop production and would otherwise import synthetic and mineral fertilizers. We also used the Simple as Necessary Baltic Long Term Large Scale (SANBALTS) model to compare eutrophication conditions for the scenarios to current and BSAP-target conditions. The scenarios suggest that reducing NANI-NAPI by redistributing manure nutrients, together with improving agronomic practices, could meet 54–82% of the N reductions targets (28–43 kt N reduction) and 38–64% P reduction targets (4–6.6 kt P reduction), depending on scenario. SANBALTS output showed that even partial fulfillment of nutrient reduction targets could have ameliorating effects on eutrophication conditions. Meeting BSAP targets will require addressing additional sources, such as sewage. A common approach to apportioning sources to external nutrients loads could enable further assessment of the feasibility of eutrophication management targets.