Recent studies highlight the fragility of the Mediterranean basin against climate stresses and the difficulties of managing the sustainable development of groundwater resources. In this work, the main issues related to groundwater management have been identified from the stakeholder’s perspective in the following four representative water-stressed Mediterranean areas: the coastal aquifer of Comacchio (Italy), the Alto Guadalentín aquifer (Spain), the alluvial aquifer of the Gediz River basin (Turkey), and the Azraq aquifer (Azraq Wetland Reserve, Jordan). This has been achieved by designing a methodology to involve and engage a representative set of stakeholders, including a questionnaire to learn their point of view concerning the current management of aquifer systems and their experience with the already available tools for groundwater resource management, such as monitoring networks and numerical models. The outcome of the survey has allowed us to identify both particular and common challenges among the four study sites and among the various groups of stakeholders. This information provides valuable insights to improve the transfer of scientific knowledge from the research centers to the authorities managing the groundwater resources and it will help to plan more effective research activities on aquifer management. The proposed methodology could be applied in other aquifers facing similar problems.