The EU Water Framework Directive (WFD) identifies diffuse pollution as a long-term threat to water quality. Farming contributes significantly to this pollution. There is a clear need for mitigation measures and assessment of their efficacy. Accordingly, Demonstration Test Catchments (DTCs) have been established in England to test the effect of changes in agricultural practice on river water quality and ecology. However, the presence of groundwater in these hydrological systems implies a wide range of travel times for pollutants from source to receptor. Unless flow routes are better characterized, it will be difficult to gauge the success of control measures in the short term. Using 3D modelling and supplementary hydrochemical information, this study considers the hydrogeology of several sub-catchments in the Avon DTC, southern England. Data suggest that groundwater ages >25 years exist in parts of the catchments; clearly, observations like these must be used to judge the likely effectiveness of targeted control measures. The revealed hydrogeological complexity of the Avon catchment is unlikely to be unique, so the techniques described here should be applicable to other lowland river systems with moderate to high baseflow indices (>0.5). To support the WFD, groundwater conceptual models should inform the design of effective measures for diffuse pollution mitigation.