An ensemble of nutrient models was applied in 17 European catchments to analyse the variation that appears after simulation of net nutrient loads and partitioning of nutrient loads at catchment scale. Eight models for N and five models for P were applied in three core catchments covering European-wide gradients in climate, topography, soil types and land use (Vansj-Hobl (Norway), Ouse (Yorkshire, UK) and Enza (Italy)). Moreover, each of the models was applied in 314 other EUROHARP catchments in order to inter-compare the outcome of the nutrient load partitioning at a wider European scale. The results of the nutrient load partitioning show a variation in the computed average annual nitrogen and phosphorus loss from agricultural land within the 17 catchments between 19.134.6 kg N ha1 and 0.121.67 kg P ha1. All the applied nutrient models show that the catchment specific variation (range and standard deviation) in the model results is lowest when simulating the net nutrient load and becomes increasingly higher for simulation of the gross nutrient loss from agricultural land and highest for the simulations of the gross nutrient loss from other diffuse sources in the core catchments. The average coefficient of variation for the model simulations of gross P loss from agricultural land is nearly twice as high (67%) as for the model simulations of gross N loss from agricultural land (40%). The variation involved in model simulations of net nutrient load and gross nutrient losses in European catchments was due to regional factors and the presence or absence of large lakes within the catchment.