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An approach to water quality control is presented for the case where there could be significant interaction of wastes in a stream. In most previous studies, a single pollutant was considered and a single related water quality parameter was used as a constraint. In highly developed river basins, it is reasonable to expect more than one important pollutant. If they interact in the stream, traditional analysis, which assumes independence, may lead to improper control policies. A free-flowing stream which receives thermal and organic wastes is modeled as an N-stage serial system. Two-dimensional dynamic programming is used to determine minimum-cost control policies. The response of total system cost and control policy to variation of quality standards is presented.