Renewable energy sources (RES) for powering desalination processes is a promising option especially in remote and arid regions where the use of conventional energy is costly or unavailable. Reverse Osmosis (RO) is one of the most suitable desalination processes to be coupled with different renewable energy sources such as solar and wind. If RES/RO systems are optimally designed, some combinations can be cost effective and reliable. However, the design of such systems is complex because of uncertain renewable energy supplies, load demands and the non-linear characteristics of some components. In such system, different scenarios can be suggested; i.e combinations of PV panels, type and number of batteries, type and number of turbines, etc. Therefore, it is difficult to determine the optimal configuration with classical techniques. The development of a tool to integrate all parameters involved and compare between the possible scenarios is very important. This paper presents a new model based on the Genetic Algorithms allowing the generation of several individuals (possible solutions) for coupling small RO unit to RES. A particular interest is focused on the hybrid systems (PV/WIND/Batteries/RO). The objective function to minimize corresponds to the total water cost (Capital cost plus Operational costs). Finally, a case study of PV/RO unit, installed since 2007 in Ksar Ghilène village in southern Tunisia, is presented.