The necessity for transitioning to renewable energy sources and the intermittent nature of the natural variables lead to the integration of storage units into these projects. In this research paper, wind turbines and solar modules are combined with pumped hydro storage, batteries, and green hydrogen. Energy management strategies are described for five different scenarios of hybrid renewable energy systems, based on single or hybrid storage technologies. The motivation is driven by grid stability issues and the limited access to fresh water in the Greek islands. A RES-based desalination unit is introduced into the hybrid system for access to low-cost fresh water. The comparison of single and hybrid storage methods, the exploitation of seawater for the simultaneous fulfillment of water for domestic and agricultural purposes, and the evaluation of different energy, economic, and environmental indices are the innovative aspects of this research work. The results show that pumped hydro storage systems can cover the energy and water demand at the minimum possible price, 0.215 EUR/kWh and 1.257 EUR/m3, while hybrid storage technologies provide better results in the loss of load probability, payback period and CO2 emissions. For the pumped hydro–hydrogen hybrid storage system, these values are 21.40%, 10.87 years, and 2297 tn/year, respectively.