This paper presents management alternatives for improving water quality in a man-made bypass canal given a local utility’s plan to increase point source discharge of highly treated domestic wastewater. In 1987, the Florida legislature enacted the Grizzle-Figg bill which presumes discharges of “recovered water” meeting advanced wastewater treatment (AWT) standards will have minimal impact on selected bays and their tributaries located in southwest Florida. Drainage basins of these selected water bodies are characterized as upland wetlands interconnected by sluggish, flowing natural tributaries leading to estuarine marshes and open bays. Historically, canals were constructed to drain wetlands for agriculture and to relieve flooding. Later, salinity barriers were constructed to prevent salt water intrusion. Today, as a preferred alternative to discharging to relatively pristine surface waters, local utilizes are planning to discharge recovered water to a flood bypass canal. Current operation of the flood control system does not consider water quality in Channel A. This paper emphasizes the best utilization of flood control structures and planned discharges of recovered water for improving water quality in Channel A. ( KEY TERMS: estuarine; wetlands; flood by-pass canal; Tampa Bay; tributaries; streamflow augmentation; marsh enhancement; effluent reuse; advanced wastewater treatment; recovered water)