A combined semi-distributed hydrological model (CASCADE/QUESTOR) is used to evaluate the steady-state that may be achieved after changes in land-use or management and to explore what additional factors need to be considered in representing catchment processes. Two rural headwater catchments of the River Derwent (North Yorkshire, UK) were studied where significant change in land-use occurred in the 1990s and the early 2000s. Much larger increases in mean nitrate concentration (55%) were observed in the catchment with significant groundwater influence (Pickering Beck) compared with the surface water-dominated catchment (13% increase). The increases in Pickering Beck were considerably greater than could be explained by the model in terms of land-use change. Consequently, the study serves to focus attention on the long-term increases in nitrate concentration reported in major UK aquifers and the ongoing and chronic impact this trend is likely to be having on surface water concentrations. For river environments, where groundwater is a source, such trends will mask the impact of measures proposed to reduce the risk of nitrate leaching from agricultural land. Model estimates of within-channel losses account for 15-40% of nitrate entering rivers.