The occurrence of phytoplankton blooms in estuarine and coastal waters is codetermined by the export of fluvial nutrients and other water properties such as turbidity. In this study, the Changjiang River Estuary was used as an example to investigate the intrinsic link between river plume dynamics, riverine nutrient loading, suspended sediment concentration, and phytoplankton blooms with a coupled hydrodynamic-sediment-ecosystem numerical model. Suspended sediment concentration from the sediment module was used to parameterize light attenuation in waters, which, in association with river plume dynamics, was found to impact phytoplankton distribution. Data that was collected in situ, in addition to satellite data for chlorophyll, nutrients, and suspended sediments, were used to validate the model, which performed well. The surface high chlorophyll centers exhibited a patch-like pattern from the northeast to the south off the Changjiang River mouth. The high chlorophyll concentration within the river plume was mainly determined by riverine nutrient exports, and potential phosphate limitation occurred away from the river mouth. The chlorophyll concentration decreased dramatically shoreward of the sediment front, which was controlled by the bottom river plume front. The bottom plume front was an intrinsic feature of the Changjiang River plume and similar river plume systems, which set a boundary separating the well-mixed (turbid) nearshore waters and stratified (clear) offshore waters. Without considering the sediment shading effect, the model yielded an unrealistic chlorophyll distribution with artificially high values in the turbid area. This indicated that light attenuation was a key factor limiting phytoplankton blooms in turbid river estuaries.Plain Language Summary In estuaries and coastal waters, the aquatic environment is affected by both riverine nutrient input and water properties such as turbidity. The associated river plume may play an essential role in controlling water properties, thus influencing the aquatic environment such as the algal blooms. In the current study, a well-validated hydrodynamic-sediment-ecosystem model was used to simulate phytoplankton blooms and the dynamic link with the Changjiang River plume. The results showed that the surface suspended sediment front was of vital importance in determining the shoreward boundary of the phytoplankton bloom area. Light attenuation due to high turbidity became a major factor limiting phytoplankton blooms in turbid nearshore waters. In environments with a strong tidal influence, the surface suspended sediment front was closely related to the bottom river plume front, which gave rise to differences in water stabilization and thus resulted in turbid conditions on either side. The results of this study provided a good reference for understanding the phytoplankton distribution characteristics in estuaries with high turbidity.