The working of superficial deposits frequently interacts with the groundwater table and thus may affect surface water and groundwater dependent terrestrial ecosystems. The Habitats Directive and the Water Framework Directive require detailed consideration of these potential effects during any application for planning consent or other authorizations and during periodic reviews. These assessments need to consider water resources impacts, the potential for pollution and whether the natural water chemistry may be changed in a way that could change ecological conditions. Early recognition of these challenges, and a well-structured hydrogeological investigation programme to properly characterize the site, is essential to facilitate timely progress through the planning process. This case study presents the approach to hydrogeological characterization and assessment used at the proposed Upwood Quarry, Oxfordshire, which is adjacent to a calcareous wetland protected at European level. Through careful characterization and stakeholder engagement, planning consent was obtained. We consider lessons that may be applied to other sites especially with increased regulation of dewatering abstractions and consider the potential impacts of recent court decisions.