This detailed study was carried out for the determination of the water cost in small size RO desalination plants in remote areas. Data from desalination plants in three Greek islands were used for a period of three years. The actual expenses for these plants were examined thoroughly and as a result the real cost per cubic meter was estimated. An evaluation of the efficiency of two different energy recovery systems was conducted by using factual operating data. The introduction of new technologies, automation, data acquisition and remote operation can be used to reduce the labor and maintenance cost for small size RO desalination plants. The increase in labor productivity has proved to be the direct result of the introduction of a low cost SCADA system to the RO plant.