This paper presents a bi-level optimization waste load allocation programming model under a fuzzy random environment to assist integrated river pollution control. Taking account of the leader-follower decision-making in the water function zones framework, the proposed approach examines the decision making feedback relationships and conflict coordination between the river basin authority and the regional Environmental Protection Agency (EPA) based on the Stackelberg-Nash equilibrium strategy. In the pollution control system, the river basin authority, as the leader, allocates equitable emissions rights to different subareas, and the then subarea EPA, as the followers, reallocates the limited resources to various functional zones to minimize pollution costs. This research also considers the uncertainty in the water pollution management, and the uncertain input information is expressed as fuzzy random variables. The proposed methodological approach is then applied to Tuojiang River in China and the bi-level linear programming model solutions are achieved using the Karush-Kuhn-Tucker condition. Based on the waste load allocation scheme results and various scenario analyses and discussion, some operational policies are proposed to assist decision makers (DMs) cope with waste load allocation problem for integrated river pollution control for the overall benefits.