The Water-Sediment Regulation Scheme (WSRS) rapidly delivers large amounts of water, sediment, and nutrients to the Yellow River Estuary (YRE) in summer (wet season). However, how these abrupt environmental changes affect phytoplankton distribution through bottom-up versus top-down control mechanisms remains poorly understood. In this study, we examined the spatiotemporal distribution of environmental drivers, grazing pressure, and phytoplankton communities in surface and bottom layers of the YRE during WSRS. Our results indicate that the WSRS transitioned phytoplankton distribution from a relatively uniform pattern pre-WSRS to a highly heterogeneous one during the sediment regulation stage. Before WSRS, phytoplankton abundance peaked near the river mouth and was co-dominated by chlorophytes, cryptophytes, and diatoms in both layers. During the water regulation stage, abundance decreased across layers, with the surface community incorporating more dinoflagellates and the bottom layer transitioning toward higher diatom and lower chlorophyte proportions. Subsequently, vertical stratification intensified during the sediment regulation stage, characterized by a chlorophytes-dominated surface hotspot (with abundance 6.8-fold higher than pre-WSRS levels) in contrast to a depauperate bottom layer. Regression tree and redundancy analysis results showed that WSRS shifts phytoplankton regulation from a bottom-up state in the pre-stage to top-down dominance during the water regulation stage, and finally to a vertically stratified regulatory state in the SR stage, with top-down control in the surface layer and bottom-up control in the bottom layer. Our findings highlight that trophic interactions and physical processes play more critical roles than previously recognized in regulating phytoplankton distribution in estuaries subjected to high-intensity hydrological disturbances.