In Europe, it is estimated that around 65 % of drinking water is extracted from groundwater. Worryingly, groundwater drought events (defined as below normal groundwater levels) pose a threat to water security. Groundwater droughts are caused by seasonal to multi-seasonal or even multi-annual episodes of meteorological drought during which the drought propagates through the river catchment into the groundwater system by mechanisms of pooling, lagging, and lengthening of the drought signals. Recent European drought events in 2010–2012, 2015 and 2017–2018 exhibited spatial coherence across large areas, thus demonstrating the need for transboundary monitoring and analysis of groundwater level fluctuations. However, such monitoring and analysis of groundwater drought at a pan-European scale is currently lacking, and so represents a gap in drought research as well as in water management capability. To address this gap, the European Groundwater Drought Initiative (GDI), a pan-European collaboration, is undertaking a large-scale data synthesis of European groundwater level data. This is being facilitated by the establishment of a new network to co-ordinate groundwater drought research across Europe. This research will deliver the first assessment of spatio-temporal changes in groundwater drought status from ∼1960 to present, and a series of case studies on groundwater drought impacts in selected temperate and semi-arid environments across Europe. Here, we describe the methods used to undertake the continental-scale status assessment, which are more widely applicable to transboundary or large-scale groundwater level analyses also in regions beyond Europe, thereby enhancing groundwater management decisions and securing water supply.