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Observations from two Bio-Argo floats deployed in the northern and central South China Sea (SCS) show distinct seasonal patterns of vertical chlorophyll distribution. There is a permanent subsurface chlorophyll maximum (SCM) located between 60 and 80 m throughout the year and a weak seasonality of surface chlorophyll in the central SCS. In the northern SCS, the SCM shoals to the upper mixed layer in winter and surface phytoplankton shows a clear winter bloom pattern. The mechanism driving the spatial and seasonal differences in phytoplankton dynamics in the euphotic zone remains unclear. Here a coupled physical-biological model is developed and applied to the northern and central SCS. With model and satellite data, we show that the contrasting patterns in chlorophyll are induced by the spatial variability in winter mixing dynamics. In the northern SCS, the buoyancy flux-induced mixing plays a dominant role in controlling the seasonal variability of vertical nutrient transport and phytoplankton production, which leads to the peak of surface chlorophyll and the significant shoaling of the SCM in winter. In the central SCS, the intensity of the buoyancy flux is reduced and both buoyancy fluxand wind-induced mixing control the winter mixing dynamics. However, the combination of these two mixing processes is weaker than in the northern SCS and the vertical nutrient transport is limited to the layer above the SCM, resulting in the reduced seasonality of surface chlorophyll and the relatively stable SCM all year round in the central SCS.Plain Language Summary Both satellite and Bio-Argo floats show a significant increase of surface chlorophyll concentration in winter in the northern South China Sea (SCS) but a very weak seasonal change in the central SCS. We used a coupled physical-biological model to systematically study the mechanism driving these spatial and seasonal differences. The model can reasonably simulate the different chlorophyll distribution patterns identified by observations. We found that the buoyancy flux-induced mixing plays a dominant role in controlling the seasonal change of chlorophyll in the northern SCS. In the central SCS, both buoyancy fluxand wind-induced mixing control the winter mixing dynamics. However, the combination of these two mixing dynamics is not as strong as that in the northern SCS and the vertical nutrient transport is only limited to the layer above the SCM, resulting in the reduced seasonality of surface chlorophyll and the relatively stable SCM all year round in the central SCS.

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The Pearl River delivers a large amount of freshwater, sediments and nutrients to the northern shelf of the South China Sea (SCS). In June 2015, an anomalously strong phytoplankton bloom was captured by satellite images in the slope region of the northern SCS, which was associated with the southeastward spreading of the river plume on the shelf and a southwestward‐moving eddy along the slope. In this study, the underlying dynamics triggering the bloom was investigated using a coupled physical‐biogeochemical model. Results show that the nutrients supporting the bloom were not directly sourced from the Pearl River, but were transported locally from subsurface. The eddy cross‐slope current advected low salinity water from the Pearl River plume, which interacted with eddy edge and enhanced frontal dynamics with vertical motions. The front‐induced upwelling injected nutrients from subsurface to surface layer and stimulated phytoplankton bloom in the upper layer. Overall, the phytoplankton bloom was attributable to the interaction of freshwater plume on top and the eddy edge induced anomaly in the subsurface. These findings suggest that the eddy‐entrained freshwater could have significant biological consequences through modifying local dynamics in the plume‐influenced region.

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Typhoons are known to induce strong ocean mixing and upwelling, bringing cold and nutrient-rich subsurface water to the surface layer. Cold subsurface water can generally lead to a decrease in sea surface temperature (SST) to the right of the typhoon track (Dickey et al., 1998;Price, 1981). The nutrient-rich subsurface water that is injected into the upper layer can stimulate phytoplankton growth and increase primary production (e.g., Babin et al., 2004;Lin et al., 2003;Walker et al., 2005). Reduced turbulence due to typhoon-induced submesoscale processes and rainfall has also been suggested to be able to induce phytoplankton blooms in the open ocean (Huang & Oey, 2015;Lin & Oey, 2016).Typhoons occur frequently in the South China Sea (SCS), with approximately 14 occurrences per year (Lin et al., 2003). In stratified seasons, phytoplankton growth in the upper layer of the SCS is generally limited due to low nutrient conditions in the open ocean (Chen et al., 2004). The passage of typhoons and the associated mixing and upwelling are thus important to the primary production and biogeochemical cycles of the SCS (G.