This investigation reports on a new national model to evaluate the effectiveness of catchment sensitive farming in England, and how pollution mitigation measures have improved water quality between 2006 and 2016. An adapted HYPE (HYdrological Predictions for the Environment) model was written to use accurate farm emissions data so that the pathway impact could be accounted for in the land phase of transport. Farm emissions were apportioned into different runoff fractions simulated in surface and soil layers, and travel time and losses were taken into account. These were derived from the regulator’s ‘catchment change matrix’ and converted to monthly load time series, combined with extensive point source load datasets. Very large flow and water quality monitoring datasets were used to calibrate the model nationally for flow, nitrogen, phosphorus, suspended sediments and faecal indicator organisms. The model was simulated with and without estimated changes to farm emissions resulting from catchment measures, and spatial and temporal changes to water quality concentrations were then assessed.