AbstractEcosystems provide a wide range of services essential for a proper environmental, economic, and social performance. While the estimated global value of ecosystem services in 2014 is very significant, the annual loss of ecosystem services value is alarming. Our paper focuses on groundwater‐dependent ecosystems (GDEs), some very important to society, which are under threat due to groundwater overexploitation. Considering the ecosystem health/status function is essential for sound groundwater regulation policy. The paper assesses the conjunctive management of groundwater and GDEs both in theory and in a relevant case study, using a certain type of an ecosystem health function. The theoretical results demonstrate how the change in the slope values of a general ecosystem health function affects the optimal groundwater management policy. The analysis also suggests a change in groundwater management strategies as a function of the value of the ecosystem. The theoretical findings are corroborated with data from an aquifer in Spain and its associated GDE—the Tablas de Daimiel Wetland. The paper highlights theoretically and empirically the necessity for a better understanding of GDEs behavior. It calls for groundwater regulation to protect these resources.