The variability of chlorophyll a concentration (Chl a) in the open South China Sea (SCS) was examined using observations from two Bio‐Argo floats. During the period of September 2014 to August 2015, there was a permanent subsurface Chl a maximum (SCM) in the depth range of 48 to 96 m in the central basin of the SCS. In the northern basin, the SCM disappeared in winter, replaced by enhanced surface layer phytoplankton with high Chl a. The values of the SCM were influenced by the vertical displacement of isotherms. Strong wind forcing and surface cooling were the main physical drivers of high surface Chl a in winter. In the north, stronger wind than in the center, lower sea surface temperature (SST) than in the center, and Kuroshio water intrusion were more favorable for the upward transport of nutrient‐rich deep water. A large amount of nitrate could be advected from the Taiwan Strait and shallow continental shelf to the northern basin in winter. A combination of strong wind mixing, surface cooling, Kuroshio water intrusion, and horizontal advection caused the winter surface phytoplankton bloom in the north.

Mesoscale eddies play a significant role in supplying the nutrients required for phytoplankton blooms and redistributing biomass in the ocean. However, how eddies influence nutrient flux and biomass distribution remains unclear. Here we reveal two important dynamical processes (radial displacement and vertical fluctuations) within an anticyclonic eddy by analyzing observations from Argo floats. The Argo floats in the eddy were displaced toward the eddy edge due to the imbalance of radial momentum. Vertical fluctuations below the mixed layer resulted in alternating upwelling and downwelling in the inner and outer parts of the eddy. High salinity deep water was uplifted tens of meters by the upwelling and further extended to the surface with the aid of wind effects. Vertical motions associated with the fluctuations penetrated to the depths of several hundred meters. These processes represent crucial dynamical mechanisms for the motion of particles in mature anticyclonic eddies.

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 flux‐ and 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.