Our daily lives depend on the provision of services by different ecosystems in which an important contribution is made by groundwater. To balance competing demands placed on groundwater for socioeconomic and ecological benefits constitute major challenges for water managers. At the policy-science interface the ecosystem service concept represents an appropriate approach to communicate management challenges in which researchers and politicians must take into account human and biophysical characteristics as intertwined systems. This study investigated the complexity of groundwater governance, and linkages between management and corresponding effects on ecosystem services. Empirical insights were derived from case studies in South Africa, Spain and Germany. The analytical focus includes (a) the degree of vertical (multi-level) and horizontal (cross-sectoral) integration which frame crucial characteristics of an adaptive governance regime and (b) the role of formal and informal institutions governing groundwater. In doing so, an conceptual and analytical approach was applied, especially developed to support a systematic and consistent investigation of policy and management processes. Evidence highlights that higher degrees of integration: (i) opens up the political arena for environmental perspectives, (ii) increases the quality of management plans, (iii) accelerates the implementation of measurements, (iv) mitigates conflicts between different groundwater users, and (v) increases the awareness of various ecosystem services. Further the results indicate that having well-crafted institutions in place does not automatically indicate successful groundwater management in the sense of bringing about positive results for socioeconomic or ecological sustainability. This work made a significant contribution to interdisciplinary research in the field of groundwater governance and ecosystem service management that builds the foundations for improving the policy-science interface.