Subsurface 3D geological models of aquifer and seal rock systems from two contrasting analogue sites have been created as the first step in an investigation into methodologies for geological storage of carbon dioxide in saline aquifers. Development of the models illustrates the utility of an integrated approach using digital techniques and expert geological knowledge to further geological understanding. The models visualize a faulted, gently dipping Permo-Triassic succession in Lincolnshire and a complex faulted and folded Devono-Carboniferous succession in eastern Scotland. The Permo-Triassic is present in the Lincolnshire model to depths of −2 km OD, and includes the aquifers of the Sherwood Sandstone and Rotliegendes groups. Model-derived thickness maps test and refine Permian palaeogeography, such as the location of a carbonate reef and its associated seaward slope, and the identification of aeolian dunes. Analysis of borehole core samples established average 2D porosity values for the Rotliegendes (16%) and Sherwood Sandstone (20%) groups, and the Zechstein (5%) and Mercia Mudstone (<10%) groups, which are favourable for aquifer and seal units respectively. Core sample analysis has revealed a complex but well understood diagenetic history. Re-interpretation of newly reprocessed seismic data in eastern Scotland has significantly reduced interpretative uncertainty of aquifer and seal units at depths of up to −6 km OD in a complex faulted and folded Devono-Carboniferous succession. Synthesis of diverse data in the 3D geological model defines a set of growth folds and faults indicative of active Viséan to Westphalian dextral-strike slip, with no major changes in structural style throughout the Carboniferous, in contrast to some published tectonic models. Average 2D porosity values are 14–17% in aquifer units and <2% in the seal unit, with a ferroan dolomite cement occluding porosity at depth.