Nitrate derived from agricultural activity is a threat to Scotland’s surface water and groundwater environment. The pollution of groundwater by nitrate can impact drinking water in aquifers in addition to the quality of base-flow to many streams and rivers. European legislation (in the form of the Nitrates Directive) requires that waters with a nitrate concentration of greater than 50 mg-NO3 l−1 (and those at risk of exceeding this concentration) should be identified and the catchment areas designated as Nitrate Vulnerable Zones (NVZs). Groundwater NVZs for Scotland were developed using a risk-based methodology which combined several Scottish national scale datasets in a GIS. The risk of nitrate leaching was determined from soil, climate and land use data. Digital solid and superficial geology data (at 1:50 000 scale) were interpreted to give an indication of aquifer vulnerability. The final zones were then determined by identifying local surface water catchments associated with areas of greatest nitrate leaching and aquifer vulnerability. The results of the vulnerability/risk analysis were broadly consistent with the available nitrate data for much of Scotland. Groundwater nitrate data were collated from the monitoring network of the Scottish Environment Protection Agency (SEPA), water authority boreholes and private water supplies, with additional new data collected from targeted sites. Within the NVZs, 25% of approximately 1700 samples exceeded 50 mg-NO3 l−1 compared to the rest of Scotland, where less than 5% of approximately 700 samples exceeded this concentration. The nitrate vulnerable zones have now been designated by the Scottish Executive and action programmes established to reduce nitrate contamination in these areas.