Unlike the motion of the air contaminants, the polluted contaminants in a river move from upstream to downstream, and a river can affect to districts more than two. In addition, a decision making on the construction of a sewage treatment facilities follows the concept of ‘economy of scale’. These reasons support the collaboration among local governments in order to reduce the costs in improving water quality. The purpose of this study is to suggest an alternative for the solution of a cost allocation issue that usually occurs at planning projects for river water quality management. As a case study, the target of reduction of BOD pollutant loadings to achieve water quality standard are BOD discharge of Pyeongdong industrial complex in Gwangju and pollutant reduction volume of Yeongbon-B watershed and Yeongbon-C watershed. The stakeholder of cost allocation are Gwangju, Jeonnam and national government. We suggested the inter-local governments cost allocation method from the case study. The theoretical approach for the cost allocation was based on the cooperative game theory, and in terms of methodology, we used the SCRB method which are comparatively easy to apply. From the study, the financial contribution of cost between Gwangju, Jeonnam and national government are approximately 183,729.4 million won (50.64%), 73,061.2 million won (20.14%), 105,998.8 million won (29.22%). This study is expected to provide an alternative for solving the similar problems of cost allocations for river water quality management in the future.