The 1991 EU Nitrate Directive was designed to reduce water pollution from agriculturally derived nitrates. England and Wales implemented this Directive by controlling agricultural activities within their most vulnerable areas termed Nitrate Vulnerable Zones. These were designated by identifying drinking water catchments (surface and groundwater), at risk from nitrate pollution. However, this method contravened the Nitrate Directive because it only protected drinking water and not all waters. In this paper, a GIS was used to identify all areas of groundwater vulnerable to nitrate pollution. This was achieved by constructing a model containing data on four characteristics: the quality of the water leaving the root zone of a piece of land; soil information; presence of low permeability superficial (drift) material; and aquifer properties. These were combined in a GIS and the various combinations converted into a measure of vulnerability using expert knowledge. Several model variants were produced using different estimates of the quality of the water leaving the root zone and contrasting methods of weighting the input data. When the final models were assessed all produced similar spatial patterns and, when verified by comparison with trend data derived from monitored nitrate concentrations, all the models were statistically significant predictors of groundwater nitrate concentrations. The best predictive model contained a model of nitrate leaching but no land use information, implying that changes in land use will not affect designations based upon this model. The relationship between nitrate levels and borehole intake depths was investigated since there was concern that the observed contrasts in nitrate levels between vulnerability categories might be reflecting differences in borehole intake depths and not actual vulnerability. However, this was not found to be statistically important. Our preferred model provides the basis for developing a new set of groundwater Nitrate Vulnerable Zones that should help England and Wales to comply with the EU Nitrate Directive.