Coastal groundwater‐dependent ecosystems (GDEs), such as wetlands, estuaries and nearshore marine habitats, are biodiversity hotspots that provide valuable ecosystem services to society. However, coastal groundwater and associated ecosystems are under threat from groundwater exploitation and depletion, as well as climate change impacts from sea‐level rise and extreme flood and drought events. Despite many well‐intentioned policies focused on sustainable groundwater use and species protection, coastal GDEs are falling through gaps generated by siloed policies and as a result, are declining in extent and ecological function. This study summarized then examined policies related to the management of coastal groundwater and connected ecosystems in two key case study areas: Queensland (Australia) and California (USA). Despite both areas being regarded as having progressive groundwater policy, our analysis revealed three universal policy gaps, including (1) a lack of recognition of the underlying groundwater system, (2) fragmented policies and complex governance structures that limit coordination, and (3) inadequate guidance for coastal GDE management. Overall, our analysis revealed that coastal GDE conservation relied heavily on inclusion within protected areas or was motivated by species recovery, meaning supporting groundwater systems remained underprotected and outside the remit of conservation efforts. To close these gaps, we consider the adoption of ecosystem‐based management principles to foster integrated governance between disparate agencies and consider management tools that bridge traditional conservation realms. Our findings advocate for comprehensive policy frameworks that holistically address the complexities of coastal GDEs across the land‐sea continuum to foster their long‐term sustainability and conservation.