Over the last 10 years, progressive development of the Guangdong-Hong Kong-Macau Greater Bay area in our country has caused rapid population growth within the Pearl River watershed. In the meantime, demand for food and energy has increased dramatically. These result an expansion of agriculture land in the upper reaches of the Pearl River catchment and an increase in the rate of urbanization in the downstream area. As a result, groundwater and surface runoff entering the Pearl River up-stream now contains higher levels of fertilizer than previous, whilst in urban areas sewage and effluent production has increased considerably. A side effect of these changes is that the amount of pollution entering the estuary in a non-point source manner has increased, leading to widespread eutrophication there. Besides, global warming increased typhoons from South China Sea and Western Pacific making landfall near the Pearl River estuary, resulting in the enhanced redistribution of anthropogenic nutrients into the oceanic water. Both in-situ and satellite have been used to investigate the impact these typhoons have on Pearl River phytoplankton dynamics. They identified four factors impacting the redistribution of phytoplankton include the vertical mixing of oceanic water, high precipitation in the watershed, the large freshwater discharge and nutrients loading, and the variation of wind fields. To date, there have been no studies address how these four factors work together to influence the distribution of chlorophyll in the Pearl River estuary. In this research, we built a land-ocean-atmosphere modeling system for the China Great Bay Area. We conducted numerous controlled experiments to examine the sensitivity of the system to multiple forcing conditions. We also investigated the effect of each controlling mechanism has on phytoplankton dynamics, using the incidence of Hurricane Hato's arrival in the area as an opportunity to collect first-hand, real-time observations. Our results show that the temporal resolution of river runoff data used in the modeling system has a profound impact on the simulation results. Using daily river runoff data from land surface models produced very different results from those using monthly data. As Hato passed by, strong onshore winds inhibited the spread of freshwater from the Pearl River, increasing the influx of seawater which in turn increased sea surface salinity and reduced the concentration of surface chlorophyll. Four days (August 27th) after Hato had passed by, water that had fallen on land as precipitation during the typhoon entered the Estuary as runoff. The dramatic increase of river discharge coincident with this event enhanced the level of nutrient loading and caused dramatic phytoplankton growth. Chlorophyll levels were still increasing two weeks after the typhoon Hato passing by (September 1st). The land-ocean-atmosphere modeling system built for the Pearl River Estuary in our research could be adapt to other estuarine and coastal regions and would ultimately help predict algal blooms, hypoxia within the aquatic environment, and other ecological hazards in the future.