Protected areas are a key tool for conserving biodiversity, sustaining ecosystem services and improving human well-being. Global initiatives that aim to expand and connect protected areas generally focus on controlling ‘above ground’ impacts such as land use, overlooking the potential for human actions in adjacent areas to affect protected areas through groundwater flow. Here we assess the potential extent of these impacts by mapping the groundwatersheds of the world’s protected areas. We find that 85% of protected areas with groundwater-dependent ecosystems have groundwatersheds that are underprotected, meaning that some portion of the groundwatershed lies outside of the protected area. Half of all protected areas have a groundwatershed with a spatial extent that lies mostly (at least 50%) outside of the protected area’s boundary. These findings highlight a widespread potential risk to protected areas from activities affecting groundwater outside protected areas, underscoring the need for groundwatershed-based conservation and management measures. Delineating groundwatersheds can catalyse needed discussions about protected area connectivity and robustness, and groundwatershed conservation and management can help protect groundwater-dependent ecosystems from external threats.