The Greek regions of Crete and of the Aegean Islands are of the southernmost river basin districts (RBDs) of the European Union. They both have limited water resources, and water demand often surpasses water availability. The geographical fractionation, particularly for the region of the Aegean Islands, is a major constrain for the implementation of an integrated water management plan. This article aims at presenting the current status of water resources in the above regions, and the existing water management plans. The article summarizes the pressures on the water resources of the above geographical regions, and investigates the possibility for utilization of non-conventional water resources, like desalinated seawater, reclaimed wastewater and brackish water. One of the conclusions among others is that the development of novel processes on water resources management should be one of the primary aims of any integrated water management plan.