The EC Nitrate Directive (91/676), agreed by the EC Environment Council in 1991, is an environmental measure designed to protect water against pollution caused by nitrate from agriculture. In 2000, the River Ythan catchment, a 68 000 ha area of predominantly agricultural land in NE Scotland, was designated a nitrate vulnerable zone (NVZ) by the Scottish Executive. A combination of reasons for designation was suggested, including evidence of elevated nitrate concentrations in the surface waters of the catchment together with the criteria set out at Annex IA(3) of the EC Nitrates Directive, i.e. that the estuary is eutrophic or in the near future may become eutrophic. Evidence from the Scottish Environment Protection Agency surface water monitoring sites has revealed several tributaries of the Ythan with nitrate concentrations exceeding the maximum permitted level of 50 mg l-1 (11.3 mg l-1 NO3-N) and a rising trend in the main river channel. There has been an approximate threefold increase in surface water nitrate concentrations since the early 1960s to a current value of ∼35 mg l-1 (8 mg l -1 NO3-N) There is separate evidence of elevated nitrate concentrations in groundwater. The amounts of fertiliser N applied annually has also increased substantially and in 1994 these were estimated to be ∼60% of the total N (equivalent to 194 kg ha-1) added to the catchment. Various stages have been involved in the decision to designate including documents for public consultation and a proposed Action Programme. However, several issues remain to be resolved, especially the extent to which a causal relationship actually exists between the increased loss of nitrate to the estuary and algal growth. Being able to accurately apportion sources of N 'supply' with periods of 'uptake' within the aquatic system is complicated. Here we suggest that an estimated 70% of the terrestrially derived nitrate input to the estuarine system actually occur out with the main period of algal growth. This emphasises the need for a greater understanding of the spatial and temporal linkages that exist between N cycling in terrestrial and aquatic ecosystems particularly as this will directly influence the likely success and cost effectiveness of remedial measures taken to relieve the symptoms of eutrophication.