Adequate hydrogeological conceptualisation of structurally complex fractured aquifers requires the support of detailed geological mapping and three dimensional understanding. With a geological framework in place uncertainties in hydrological understanding and irregularities in hydraulic observations may be rationalised. Using the Cotswold of southern England, which are underlain by the ooidal limestone-dominated Middle Jurassic Inferior Oolite and Great Oolite groups, 3D modelling software GSI3D and Geographical Information Systems (GIS) have been used to integrate observed hydraulic behaviours with the 3D geological framework. In this way a conceptual model is developed to assist simulation of groundwater flow and the predicted response of groundwater levels and river flows to climatic extremes. The structural and lithological complexity of the bedrock results in sub-catchments which exhibit individual hydraulic responses and a hydrogeological setting dominated by shallow rapid fracture pathways and copious spring discharge.