This paper presents the application of multi-criteria decision analysis to select the best energy efficient option for a water supply system. The case study is a part of the Multi-Municipal Water Supply System (MMWSS) for the Algarve region in Portugal. There is a micro-hydropower plant installed in one of the two water treatment plants. The system has two operating schemes due to the seasonality of tourism: one for the high season from June to September; and the other one for the low season from October to May. The aim of the analysis is to compare the energy efficiency of the system for the two operating schemes and for different demands. Energy audits (i.e., hydraulic energy balance along the pipe system) are carried out for each option (pair operating scheme – demand). Different energy efficiency metrics are calculated and two different multi-criteria analysis methods are used and compared to rank the options. Results obtained are discussed and the main conclusions are presented.