Seawater reverse osmosis (SWRO) desalination units coupled with renewable energy technologies such as photovoltaics are a very appealing suggestion, especially in remote areas, such as islands and coastal regions, which often face lack or low quality fresh water coupled with electrical energy shortages. This paper regards an experimental investigation of a PV powered small-scale SWRO desalination system which employs hydraulic energy recovery, based on a DC microgrid concept and incorporates a short term electric energy storage in the form of hybrid capacitors and a short term hydraulic energy storage in the form of pressure vessels. A multi agent decentralized energy management system which relies on intelligent agents and employs Fuzzy Cognitive Maps for its implementation, allowing for efficient operation of the desalination system under variable conditions (variable feed pressure), was developed and implemented. The experimental results show that it is feasible to operate efficiently such PV powered SWRO system. Furthermore, the desalination unit produces potable water during daytime even at periods when the produced energy from the PV array is not sufficient to operate the desalination unit. Moreover, the SWRO system shows a continuous and smooth operation, meaning small feed water pressure variations at sharp rapid solar irradiation intensity variations due to the incorporated short-term storage. In addition, the intelligently managed PV powered SWRO system with short term storage produces considerably more fresh water, especially at days with variable solar irradiation, as compared to the same SWRO system directly PV driven without storage and any control.