This study describes a source apportionment methodology for nitrogen river transport. A statistical model has been developed to determine the contribution of each source (punctual and diffuse) of nitrogen to river-mouth transport. A non-linear regression equation was developed, relating measured nitrogen transport rates in streams to spatially referenced nitrogen sources and basin characteristics. The model considers applied fertilizer, atmospheric deposition and point discharges as sources, and winter rainfall, average air temperature, topographic wetness index and dry season flow as basin characteristics. The model was calibrated in an area of 8913 km2 in East Anglia (UK). In the studied area, the average contribution of agriculture to the nitrogen load is estimated around 71%. Point sources and atmospheric deposition respectively account for 24% and 5% of the exported nitrogen. The model allowed the estimation of the contribution of each source to nitrogen emissions and the nitrogen retention in soils and waters as influenced by basin factors.