A multi-scale study has been undertaken to explore the relationships between climate, water resources, land use and diffuse pollution in order to assess the significance of projected future changes in climate and the uncertainty inherent in these projections. Two climate simulations from the GCM-RCM Perturbed Physics Ensemble developed by the UK Met Office Hadley Centre, broadly representing the extremes of future climate simulations, were downscaled and applied to a grid-based dynamic national water balance and nitrate model for Scotland. Results from this model were cross-compared with multiple simulations using synthetic future climate data generated by the 2009 UK Climate Projections Weather Generator (WG) for two selected catchments. At a national scale the model predicted relatively small effects of climate change in terms of spatially and temporally averaged means, but with significant regional variability. Future changes in the seasonality of nitrate losses were also predicted, but with a high degree of uncertainty as to the scale of this change demonstrated by the different climate simulations. A land use scenario was developed in which food security is a very high priority for Scotland and this was linked with a classification of future land capability. Application of this scenario with the national scale model indicated greater changes in nitrate pollution caused by the land use change than those caused by the direct impacts of climate change on hydrological functioning. The multiple climate simulations applied at a catchment scale demonstrated that the two national scale simulations broadly represent likely bounds in future climate, although a probability figure cannot be assigned to them.