This paper uses the grey fuzzy multiobjective programming to aid in decision making for the allocation of waste load in a river system under versatile uncertainties and risks. It differs from previous studies by considering a multicriteria objective function with combined grey and fuzzy messages under a cost benefit analysis framework. Such analysis technically integrates the prior information of water quality models, water quality standards, wastewater treatment costs, and potential benefits gained via in-stream water quality improvement. While fuzzy sets are characterized based on semantic and cognitive vagueness in decision making, grey numbers can delineate measurement errors in data collection. By employing three distinct set theoretic fuzzy operators, the synergy of grey and fuzzy implications may smoothly characterize the prescribed management complexity. With the aid of genetic algorithm in the solution procedure, the modeling outputs contribute to the development of an effective waste load allocation and reduction scheme for tributaries in this subwatershed located in the lower Tseng-Wen River Basin, South Taiwan. Research findings indicate that the inclusion of three fuzzy set theoretic operators in decision analysis may delineate different tradeoffs in decision making due to varying changes, transformations, and movements of waste load in association with land use pattern within the watershed.