Under the Water Framework Directive (WFD) the requirement for ‘good groundwater status’ is dependent upon there being no ‘significant damage’ to groundwater-dependent terrestrial ecosystems, i.e. groundwater-dependent wetlands. An ecohydrogeological framework was developed to assess the risk of significant damage for groundwater-dependent terrestrial ecosystems in the UK and the Republic of Ireland. The framework will be used by the competent authorities implementing the WFD as a decision support system to apply the WFD guidelines on a local to regional basis. The framework considers the variety of groundwater controls and pathways of different wetland types and allows a specific assessment to be made of the vulnerability of different wetland types to groundwater related risks. Seven distinct wetland types were identified and the potential pressures were evaluated. A GIS framework was developed in order to analyse the spatial coincidence of potential risks to each wetland type. The framework was tested for a trial dataset of 10 groundwater controlled wetland ecosystems in England and Wales in order to evaluate their current risk of damage.