Effective water governance is the key to achieving water security and sustainable water management. This study promotes water efficiency and supports the shift towards climate-resilient agriculture in Mediterranean countries through the development and implementation of water management adaptation strategies in three Farmers’ Organizations (F.ORs) located in Mediterranean areas. An integrated water governance scheme is presented, which can be applied at the F.OR level for a more effective implementation of the water management adaptation strategy. The proposed water governance scheme has been adopted by three F.ORs (two in Crete, Greece, and one in Basilicata, Italy). The water management system that is developed as a tool for the implementation is presented, and the lessons learnt during the implementation are discussed. Experience from the pilot implementation of the proposed strategy in the three participating F.ORs indicated that systematic monitoring and evaluation of the strategy can increase the implementation efficiency and save resources. Moreover, the significance of internal dissemination and transparency was highlighted. The result of this study is the proposed integrated water governance scheme, which constitutes a valuable tool for F.ORs’ adaptation to climate change in terms of water efficiency.