This paper is concerned with the application of optimal control techniques to ecological systems. In particular, the control of pollution of water in a river stream is considered. The variables to be controlled are the concentration of Biochemical Oxygen Demand (BOD) and the level of Dissolved Oxygen (DO) in the water. This is proposed to be achieved by controlled dumping of industrial effluents and/or artificial aeration. These constitute the controls. A realistic determination of the optimum values of these controls is subject to several performance criteria relating to water quality. Since some of these criteria are contradictory the problem is tackled (unlike previous investigators) from the point of view of a multi-cost system. Recently published theory on multi-cost system optimization is used. Numerical examples are presented.