The development of an attributed 3D model of the Quaternary deposits across 75 km2 of central Manchester and Salford is providing a basis for new types of applied (thematic) outputs. Proprietary software designed specifically for use in Quaternary sequences has been used to construct a model of the glacial and post-glacial sequences in an area now undergoing rapid regeneration. The potential of the model to deliver information relevant to a range of practical applications is illustrated by an urban groundwater case study centred on the industrial area of Trafford Park. The sensitivity of the Permo-Triassic sandstone bedrock aquifer to pollution and the extent to which recharge may occur have been analysed through detailed characterization of the underlying superficial deposits. Potential hydrogeological pathways from ground surface to the sandstone are identified, and thematic outputs show the importance of the Manchester Ship Canal and related waterways as potential sources of recharge and pollution of the bedrock aquifer. The move towards 3D modelling of the shallow subsurface provides flexibility in meeting user needs that is not available from conventional 2D geological sources. It is suggested that modelling of this type should be used by site developers and remediators to design more targeted and cost-effective site investigations and risk assessments.