In this paper, a new methodology is proposed for waste load allocation in river systems using the decision support system (DSS) for the graph model for conflict resolution II (GMCRII), multi-criteria decision making (MCDM) analysis and the Multi-Objective Particle Swarm Optimization (MOPSO) algorithm. Minimization of total treatment and penalty costs and minimization of biological oxygen demand violation of standards at the check point are considered as the main objectives of this study. At first, the water quality along the river was simulated using the Streeter-Phelps (S-P) equation coupled with the MOPSO model. Thereby a trade-off curve between the objectives is obtained and a set of non-dominated solutions is selected. In the next step, the best alternative is chosen using MCDM techniques and the GMCRII DSS package and non-cooperative stability definitions. The applicability and efficiency of the methodology are examined in a real-world case study of the Sefidrud River in the northern part of Iran.