Nutrient pollution of air and water is a persistent problem in Europe. However, the pollution sources are often analyzed separately, preventing the formulation of integrative solutions. This study aimed to quantify the contribution of agriculture to air, river and coastal water pollution by nutrients. A new MARINA-Nutrients model was developed for Europe to calculate inputs of nitrogen (N) and phosphorus (P) to land and rivers, N emissions to air, and nutrient export to seas by river basins. Under current practice, inputs of N and P to land were 34.4 and 1.8 Tg·yr^–1, respectively. However, only 12% of N and 3% of P reached the rivers. Agriculture was responsible for 55% of N and sewage for 67% of P in rivers. Reactive N emissions to air from agriculture were calculated at 4.0 Tg·yr^–1. Almost two-fifths of N emissions to air were from animal housing and storage. Nearly a third of the basin area was considered as pollution hotspots and generated over half of N emissions to air and nutrient pollution in rivers. Over 25% of river export of N ended up in the Atlantic Ocean and of P in the Mediterranean Sea. These results could support environmental policies to reduce both air and water pollution simultaneously, and avoid pollution swapping.