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This paper studies the distributed control of network flows using an embedded sensor-actuator network. We focus on the problem of reducing the frequency of combined sewer overflow (CSO) events in city sewer systems. This is an important environmental problem whose cost effective solution is of great interest across the world. Our approach embeds microprocessor controlled sensors and actuators directly into the sewer network. These embedded processors communicate with each other over a multi-hop communication network whose topology follows the topology of the sewer network. We use Pontryagin's maximum principle to develop a switching control where control decisions are made in a distributed manner. We present simulation results showing that the proposed method has the potential of greatly reducing the frequency of CSO events over existing passive thresholding strategies.