Managing diffuse pollution in catchments is a major issue for environmental managers planning to meet water quality standards and comply with the EU Water Framework Directive. A major source of diffuse pollution is from nitrogen, with high nitrate concentrations affecting water supplies and in-stream ecology. A dynamic, process based model of flow, nitrate and ammonium (INCA-N) has been applied to the Hampshire Avon as part of the NERC Macronutrient Cycles Programme to link upstream and downstream measurements of water chemistry. The model has been calibrated and validated against Environment Agency discharge and solute chemistry data, as well as a data set collected from a river site immediately upstream of the estuary tidal limit. Upstream measurements of denitrification at six sites have been used to evaluate nitrate removal rates in vegetated and non-vegetated conditions. Results show that sediments underlying vegetation were associated with significantly higher rates of nitrate removal than un-vegetated sediments (with an average increase of 245%). These data have been used to scale up rates of nitrate loss to the whole catchment scale and have been implemented via the model. The effects of streambed geology and macrophyte cover on catchment-scale nitrogen dynamics are explored and nutrient fluxes entering the estuary are evaluated. The model is used to test a strategy for nitrogen reduction assessed using a nitrate vulnerable zone (NVZ) methodology. It suggests that nitrate and ammonium concentrations could be reduced by 10% in 10 years and much lower nitrogen level can be achieved but only over a long time period.