Integrated management systems (IMS) that control entire sewerage facilities in the upper reaches of multi-purpose dams are being constructed for their efficient operation and management. However, because the IMS installed in a watershed belong to several local government bodies, significant conflict would be expected between stakeholders in the process of deciding who should control the IMS after completion of the construction that was initially implemented under the support of central government. The objective of this study was to suggest a decision making to determine who should control the IMS for sewerage facilities in the upper reaches of multipurpose dams in Korea, using the analytic hierarchy process (AHP). Three alternatives were selected to determine who should control the IMS for sewerage facilities: commissioning to public corporations, commissioning to private corporations, and a role-sharing partnership. In using the AHP technique, the emphasis was on comparing public interests, economics, efficiency, sustainability, specialty, grievance mediation and receptiveness. As a result, building a role-sharing partnership received the highest score. Commissioning to a special institute was also suggested as an alternative as this showed a score similar to that of building a role-sharing partnership.