One of the challenging issues in designing and operation of inter-basin water transfer systems is quantifying the relative power of water users. In this paper, a comprehensive set of criteria including regional gross income, water efficiency, presence of alternative water resources, self-sufficiency, existence of agricultural and industrial infrastructures, receiving political support of the government and parliament, and preference-based power is proposed to determine the power of water users in a quantitative way. Then, some well-known Multiple Criteria Decision Making (MCDM) methods, namely Analytical Hierarchy Process (AHP), Analytical Network Process (ANP), Evidential Reasoning (ER), Method for Order Preference by Similarity to Ideal Situation (TOPSIS) and Preference Ranking Organization Method for Enrichment Evaluations (PROMETHEE II), are utilized to evaluate the power of water users in inter-basin water allocation systems. In this paper, the Spearman’s rank correlation coefficient and Kendall’s coefficient of concordance are applied to compare the ranking outputs resulting from different MCDM methods. At last, the proposed approach is applied to a large-scale case study of water transfer from the Karoon River basin to the Rafsanjan plain in the central part of Iran.