Fecal coliform are widely used as bacterial indicator in the United States and around the world. Fecal coliform impaired water is highly possible to be polluted by pathogenic bacteria. The Tidal Basin and Washington Channel in Washington, DC are on the Total Maximum Daily Load (TMDL) list due to the high fecal coliform level. To support TMDL development, a three-dimensional numerical model of fecal coliform was developed using the EFDC framework. The model calculates the transport of fecal coliform under the influences of flap gate operations and tidal elevation. The original EFDC code was modified to calculate the die-off of fecal coliform under the impact of temperature and solar radiation intensity. The watershed contribution is expressed as storm water inflow and the load carried by the runoff. Model results show that fecal coliform vary strongly in space in both the Tidal Basin and Washington Channel. The storm water only impacts a small area around the storm water outfall in the Tidal Basin and the impacts are negligible in the Washington Channel due to dilution. The water from the Potomac River may affect the fecal coliform level in the area close to the flap gate in the Tidal Basin. The fecal coliform level in the Washington Channel is mainly controlled by the fecal coliform level in the Anacostia River, which is located at the open boundary of the Washington Channel. The potential sediment layer storage of fecal coliform was analyzed and it was found that the sediment layer fecal coliform level could be much higher than the water column fecal coliform level and becomes a secondary source under high bottom shear stress condition. The developed model built solid connection of fecal coliform source and concentration in the water column and has been used to develop TMDL.