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We validated an existing physically based 3D MIKE SHE groundwater resource model (DK-model) at 175 Danish gauging stations covering different catchment sizes in order to calculate monthly water runoff in the 50% ungauged part of Denmark. Model performance was in most cases good (61% of gauging stations had a Nash–Sutcliffe (NS) coefficient >0.60) but nevertheless showed a large seasonal and georegion specific bias. Therefore, bias correction factors had to be developed before applying the DK-model simulations of runoff in the ungauged areas. Simulated monthly runoff from ungauged areas and the measured monthly runoff from 178 gauging stations were distributed to 2663 smaller Hydrological Units (ca.15 km2) and linked with a new empirical model for flow-weighted monthly total nitrogen (TN) concentrations (R2= 0.43; P25% of the observations of monthly discharge weighted TN concentrations a NS larger than 0.26. Catchment specific monthly TN-loadings were modelled with a higher performance as 50% of the catchments had a NS greater than 0.75. The model concept allows calculation of N retention in streams, lakes and wetlands and the average annual model calculated N retention amounted to 21% of the modelled gross riverine TN loadings. The average annual gross TN loading to surface freshwater in Denmark derived from diffuse sources amounted to 97 000 tonnes N (91% of gross TN loadings) which is 54% of the total estimated N-leaching from the root zone on the Danish land area (212 000 tonnes N) during the period 1990–2009. [ABSTRACT FROM AUTHOR]