The upper 40-mile reach of the Potomac Estuary is modeled by a nonlinear, time variable representation of phytoplankton dynamics. Nitrogen and phosphorous recycling is included. Sensitivity analyses indicate that phytoplankton from tidal embayments can contribute as much as 40 μg/l to observed chlorophyll in the main channel. Loss of phosphorous to the sediments is significant. Flow transport through the estuary and the nutrients and phytoplankton associated with increasing river flow are particularly important. Simulations indicate that under nondrought flows and a 90% reduction of untreated nutrient loads, chlorophyll concentrations in the main channel may rise to 50 μg/l and to 70 μg/l in tidal embayments. These concentrations are above an objective of 25 μg/l, but are about 60% less than present values.