Two models, N_EXRET and INCA, were applied to the Simojoki river basin (3160 km2) in northern Finland in order to assess nitrogen retention in wetlands and lakes. N_EXRET is a spatial, export coefficient-based N export and retention model developed for large river basins. It utilizes remote sensing-based land use and forest classification, evaluated export coefficients, and data on areal N deposition and point sources of N. A new version (v1.7) of the Integrated Nitrogen in CAtchments model (INCA) is a semi-distributed, dynamic nitrogen process model, which simulates and predicts nitrogen transport and processes within catchments. Average retention of the gross total N load of 700 t a−1to the river system was estimated using N_EXRET model as 17 t N a−1to the wetlands and 77 t N a−1to the lakes. A good fit was found between modeled and measured values along the river. Inorganic N fluxes simulated by the INCA model were compared with measured fluxes along the river Simojoki, with a good fit between modeled and measured NH4+-N fluxes, and an adequate fit for NO3−-N fluxes. Both fluxes were overestimated at the first reach, below Lake Simojärvi. High percentage of peatlands led to high NH4+-N/NO3−-N ratios derived from data, indicating negligible nitrification in large river subbasins and particularly in small research catchments.