During the last decades human activity has altered the natural cycle of nitrogen and phosphorus on a global scale, producing significant emissions to waters. In Europe, the amount of nutrients discharged from rivers to coastal waters as well as the effects of mitigation measures in place are known only partially, with no consistent temporal and spatial cover. In this study, we quantify the loads and concentration of nitrogen and phosphorus discharged in the European seas over the period 1985–2005, and we discuss their impact on coastal ecosystems. To support our analysis, a catchment database covering the whole of Europe was developed together with data layers of nutrients diffuse and point sources, and the statistical model green was used to estimate the annual loads of nitrogen and phosphorus discharged in all European seas. The results of this study show that during the last 20 years, Europe has discharged 4.1–4.8 Tg yr−1 of nitrogen and 0.2–0.3 Tg yr−1 of phosphorus to its coastal waters. We show that beside the North Sea and part of the Baltic Sea, annual nutrient exports have not changed significantly, in spite of the implementation of measures to reduce nutrient sources, and that the N : P ratio has increased steadily, especially in the North, Mediterranean and Atlantic seas. The response of river basins to changes in inputs was not linear, but influenced by climatic variations and nutrients previously accumulated in soils and aquifers. An analysis of the effects of European environmental policies shows that measures to reduce phosphorus were more successful that those tackling nitrogen and that policies aimed at point sources were more effective or more effectively implemented than those controlling pollution from diffuse sources. The increase of the N : P ratio could fuel eutrophication in N-limited coastal ecosystems, reducing biodiversity and the ecosystem's resilience to future additional anthropogenic stress, such as climate change.