Phytoplankton biomass in estuaries is controlled by complex biological and chemical processes that control growth and mortality, and physical processes that control transport and dilution. The effects of these processes on phytoplankton blooms were systematically analyzed, focusing on identifying the dominant controlling factors out of river-induced flushing, tidal dispersion, nutrient limitation, and light limitation. To capture the physical processes related to flow and sediment dynamics, we used the idealized width-averaged iFlow model. The model was extended with a nutrient-phytoplankton module to capture the essential biological-chemical processes. The model was applied to the Delaware River Estuary for the productive months of March to November. Model results were compared with field observations. It was found that phytoplankton blooms cannot form in the lower bay due to tidal dispersion, as water from the estuary and coastal ocean mix in early spring, and due to local effects of nitrogen limitation in summer. In the middle to upper bay, sediment-induced deterioration of the light climate limits the growth but allows for blooms in the mid bay, while no blooms can form in the turbidity maximum zone in the upper estuary. Further upstream in the tidal river, the effects of river-induced flushing dominate in early spring and prevent bloom formation. In the summer and fall, lower river discharges and higher growth rates at higher temperatures allow blooms to form and persist. Analysis of the connectivity between mid bay and tidal river blooms showed that coastal ocean phytoplankton may contribute to mid bay blooms, but do not penetrate beyond the turbidity maximum zone.