Agricultural nitrogen surplus is the main non-point source of nitrates in groundwater and thus accounts for the most sustaining component of the surface waters nitrogen load. To analyse the underlying processes at the catchment scale, an efficient GIS-based approach has been developed called MODEST - Modelling Diffuse Entries via Subsurface Trails. Grid techniques allow for process-oriented distributed modelling the long-term transport and degradation of dissolved nitrate along the underground passage through the unconsolidated rock region. Highly differentiated regional studies are feasible with reasonable computing time. A database has been compiled for the transnational Odra Basin containing digital information of land use, nitrogen balance, water budget, soils, groundwater table, and the river network. MODEST was calibrated and validated using calculated historical nitrogen balances as well as discharge values and N concentrations recently measured in rivers of selected catchments between 500 and 5,000 km2 in Poland and Germany. Case studies were performed for the present state of subsurface nonpoint source nitrogen flows in the Odra River basin and for scenarios with modified nitrogen surplus. Results have been evaluated in terms of the nitrogen load potentially to be received by the rivers.