Intensive agriculture and densely populated areas represent major sources of nutrient pollution for European inland and coastal waters, altering the aquatic ecosystems and affecting their capacity to provide ecosystem services and support economic activities. Ambitious water policies are in place in the European Union (EU) for protecting and restoring aquatic ecosystems under the Water Framework Directive and the Marine Strategy Framework Directive. This research quantified the current pressures of point and diffuse nitrogen and phosphorus emissions to European fresh and coastal waters (2005–2012), and analysed the effects of three policy scenarios of nutrient reduction: 1) the application of measures currently planned in the Rural Development Programmes and under the Urban Waste Water Treatment Directive (UWWTD); 2) the full implementation of the UWWTD and the absence of derogations in the Nitrates Directive; 3) high reduction of nutrient, using best technologies in wastewaters treatment and optimal fertilisation in agriculture. The results of the study show that for the period 2005–2012, the nitrogen load to European seas was 3.3–4.1 TgN/y and the phosphorus load was 0.26–0.30 TgP/y. Policy measures supporting technological improvements (third scenario) could decrease the nutrient export to the seas up to 14% for nitrogen and 20% for phosphorus, improving the ecological status of rivers and lakes, but widening the nutrient imbalance in coastal ecosystems (i.e. increasing nitrogen availability with respect to phosphorus), affecting eutrophication. Further nutrient reductions could be possible by a combination of measures especially in the agricultural sector. However, without tackling current agricultural production and consumption system, the reduction might not be sufficient for achieving the goals of EU water policy in some regions. The study analysed the expected changes and the source contribution in different European regional seas, and highlights the advantages of addressing the land-sea dynamics, checking the coherence of measures taken under different policies.