The important energy requirements for the desalination process impose especially in autonomous and decentralized plants supplied by Renewable Energy Sources (RES). In this paper, five alternative energy generation topologies of Reverse Osmosis desalination process are evaluated. The proposed topologies assessed in terms of economic, environmental, technological and societal indices are compared using multi-criteria analysis, namely the Analytic Hierarchy Process (AHP) and the Preference Ranking Organization Method for Enrichment of Evaluations (PROMETHEE). Ranking of topologies resulted in the selection of direct connection and hybrid configuration as optimum solutions. In case economic priorities prevail diesel generation should also be considered.