Since the early 1940s, European agriculture has intensified greatly, resulting in large inputs of nitrogen (N) and phosphorus (P) to soil by fertilizers and manure. This has led to an increase in crop growth and soil fertility in terms of elevated N and P contents. However, the increased application of fertilizers and manure also induced adverse effects, such as: (i) loss of biodiversity in natural ecosystems due to increased emission and deposition of ammonia, (ii) increased levels of nitrogen in drinking water reservoirs due to leaching of nitrate to ground water and (iii) eutrophication of surface waters due to increased runoff of N and P. Main aim of this study therefore was to identify regions where N and P loads used for agricultural production lead to the adverse impacts listed above. This was assessed by comparing current N and P losses from agriculture with critical losses, calculated at a high spatial resolution for the entire European Union using the INTEGRATOR model. Current N and P losses were based on calculations using current detailed agronomic and biophysical data. Critical N and P losses were based on critical NH3 emissions, NO3 leaching rates, as well as N and P runoff rates. Critical NH3 emissions were related to national emission ceilings in view of biodiversity loss. Critical leaching and runoff levels were derived from critical N and P concentrations in view of drinking water quality and eutrophication, respectively. Calculated current (2010) N and P balances show that they are highly spatially variable and largely related to the livestock distribution. The critical P runoff to surface waters is most often exceeded followed by N runoff to surface waters and NO3 leaching to groundwater.