Across the EU, programmes of measures have been introduced as part of river basin management planning as a means of tackling problems of diffuse pollution from agriculture. Evidence is required to demonstrate the effectiveness of these measures and with this overarching objective, monitoring of an agricultural catchment in Eastern Scotland was initiated in 2007. As a precursor to evaluating the effect of new management measures it is essential to understand how other factors, including hydrology and land use changes, could have influenced water quality. This study undertook an analysis of the trends in concentrations and loads of nitrate, soluble reactive phosphorus (SRP), suspended solids (SS) and turbidity measured at six points in the catchment over a six year period. The results identified both differing trends between determinands and differing trends occurring over varying spatial scales. The only direct relationships between land use and water quality that could be identified based on annual data was a positive link between arable cropping and nitrate concentrations. At the sub-catchment scale some temporal changes in land use and management explained short-term trends in nitrate but not in SRP. Lags in the system were identified due to soil adsorption, in-stream/loch processing and groundwater transport making the identification of cause and effect problematic. The results have implications for the demonstration of effectiveness of measures over the shorter term and the timescales of recovery from diffuse pollution. Longer term monitoring at small scales will be important in this regard.