The South Slough Estuary is located off Coos Bay along the southern coast of Oregon. It is divided into two channels that meet and continue to Coos Bay at the Charleston Harbor. There are six major contributing streams to South Slough. After rainfall events, the level of coliform bacteria in the slough increases because of stream bacteria loading. This is due to cattle grazing in the drainage areas, failed septic systems from private homes, and sewage sludge applied to the County landfill, which drains into the slough. The Oregon Health Division has enforced a Sanitation Management Plan for Commercial Shellfish Harvesting in South Slough that specifies closure of commercial shellfish harvesting for certain rainfall and flood events. The purpose of this study is to analyze and improve the current understanding of the hydraulics and water quality of the South Slough Estuary. This was achieved by calibrating the South Slough using the water quality model CEQUAL- W2. It was calibrated for the following parameters water surface elevations, velocity, temperature and total dissolved solids. A management analysis was also done analyzing the transport of bacteria and a conservative tracer. Model predictions for water surface elevations at one of the monitoring sites, Hinch Road Bridge, was significantly lower than measured elevations. There was an excellent correlation of velocity, and reasonable timing of peaks due to tidal effects. Model predictions for temperature and total dissolved solids match measured values well. To improve the accuracy of the model the following was recommended; install a raingage in the South Slough, measure temperature and constituent concentrations at inflow locations, survey the S4 current meter, new soundings performed of the Winchester Creek arm and at the Hinch Road Bridge gaging station, and investigate the possibility of an obstruction near the Hinch Road Bridge gaging station.