Agriculture is an important source of nitrogen and phosphorous loads to the Baltic Sea. We study how the European Union’s (EU) Common Agricultural Policy (CAP), and in particular how its first pillar, containing most of the budget and the decoupled farm payments, affects eutrophication. To aid our study, we use three simulation models, covering the agricultural sector in the EU, a hydrological nutrient flow model and a model of eutrophication in the Baltic Sea. We compute changes in key eutrophication indicators in a business-as-usual baseline and in a hypothetical situation where the first pillar of the CAP, containing the direct payments, greening and accompanying measures, is not present. Comparing the outcomes, we find that in the scenario without the first pillar, production and agricultural land use is lower, while yields and fertiliser use per hectare are higher, causing less nitrogen and phosphorous loads (0.5 to 4% depending on the basin) and less eutrophication in the Baltic Sea as net effect. We therefore conclude that the policies of the first pillar of the CAP contribute to increased eutrophication in the Baltic Sea.