In this study, the effects of non-uniform flow due to: (i) inflow from tributaries and (ii) the presence of a downstream control structure (such as a weir or a barrage), on the optimal waste load allocation decision and the resulting cost-equity trade-off relationships, have been investigated. These effects are illustrated with in the framework of a typical cost-equity multi-objective optimization model for optimal waste load allocation in rivers. This framework consists of an embedded river water quality simulator with gradually varied flow and transport (BOD-DO) modules and a cost-equity multi-objective optimization model. A multi-objective evolutionary algorithm known as Non-dominated Sorting Genetic Algorithm-II is used for solving the optimization problem. The optimal fraction removal levels, the treatment cost and the system inequity measure are under predicted in certain reaches of the river, if the uniform flow assumption is made, while actually non-uniform flow conditions exist. This effect is quite pronounced when the flow non-uniformity results from a downstream control structure such as a weir. © Springer Science + Business Media, Inc. 2006.