Phytoplankton phenology is a sentinel of aquatic ecosystem change, with long-term shifts often attributed to changing anthropogenic nutrient loading. Yet, when we analyzed two decades of monitoring data from a subtropical coastal system adjacent to the Pearl River estuary, we found an anomaly that deviates from this nutrient-centric view. While most regions exhibited stable seasonal cycles driven by bottom-up forcing (light, temperature, nutrients), Deep Bay, a heavily urbanized embayment where oyster farming expanded ~4-fold, tells a different story. Here, the historic summer chlorophyll peak (June–August) has crashed in magnitude and shifted earlier to May–July, decoupling from the optimal environmental window. Critically, this shift cannot be explained by changes in bottom-up conditions alone. Using a coupled biogeochemical–Dynamic Energy Budget model, we demonstrate that intensified filter-feeding by oysters is the primary driver. Our findings reveal that shellfish aquaculture can override bottom-up control, fundamentally reshaping phytoplankton seasonality. This has profound implications for coastal food webs, eutrophication management, and sustainable mariculture expansion worldwide.