This paper identifies the best energy management strategy of hybrid photovoltaic–diesel battery-based water desalination systems in isolated regions using technical, economic and techno– economic criteria. The employed procedures include Criteria Importance Through Intercriteria Correlation (CRITIC) and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) as tools for the solution. Twelve alternatives, containing three–four energy management strategies; four energy management strategies, load following (LF), cycle charging (CC), combined LF–CC, and predictive strategy; and three different sizes of brackish water reverse osmosis (BWRO) water desalination units, BWRO-150, BWRO-250, and BWRO-500, are investigated with capacity of 150, 250, and 500 m3/day, respectively. Eight attributes comprising different technical and economic metrics are considered during the evaluation procedure. HOMER Pro® software is utilized to perform the simulation and optimization. The main findings confirmed that the best energy management strategies are predictive strategies and the reverse osmosis (RO) unit’s optimal size is RO-250. For such an option, the annual operating cost and initial costs are $4590 and $78,435, respectively, whereas the cost of energy is $0.156/kWh. The excess energy and unmet loads are 27,532 kWh and 20.3 kWh, respectively. The breakeven grid extension distance and the amount of CO2 are 6.02 km and 14,289 kg per year, respectively. Compared with CC–RO-150, the amount of CO2 has been sharply decreased by 61.2%.