An environmental concern with hydraulic fracturing (fracking) is that injected fluids or formation fluids could migrate upwards along high-permeability faults and contaminate shallow groundwater resources. However, numerical modelling has suggested that compartmentalisation by low-permeability faults may be a greater risk factor to shallow aquifers than high-permeability faults because lateral groundwater flow is reduced and upward flow through strata may be encouraged. Therefore, it is important that compartmentalisation can be adequately identified prior to fracking. As a case study we used historical groundwater quality data and two-dimensional seismic reflection data from the Bowland Basin, northwest England, to investigate if compartmentalisation could be adequately identified in a prospective shale basin. Five groundwater properties were spatially autocorrelated and interpolation suggests a regional trend from recent (<10 000 years old) meteoric groundwater in the upland Forest of Bowland to more brackish groundwater across the Fylde plain. Principal components analysis suggests two end-member brackish groundwater types. These end-members along with seismic interpretation suggest that a fault may structurally compartmentalise the northwest Bowland Basin. Furthermore, the Woodsfold fault structurally compartmentalises the southern Fylde and the Blackpool area provides evidence for stratigraphic compartmentalisation in the superficial deposits. However, large areas of the Bowland Basin are not sampled and the influence of known faults on groundwater is therefore difficult to assess. Consequently, the adequate identification of compartmentalisation in prospective basins may require supplementing historic data with dedicated basin-wide groundwater monitoring programmes and the acquisition of new seismic reflection data in areas of poor coverage or quality.