Time series data from a sediment trap at approximately 1,000‐m depth in the northwestern South China Sea, July 2012 to April 2013, were used in combination with remote sensing and shipboard physical and biogeochemical data to quantify the effects of multiscale physical processes on sinking particle fluxes and the function of the local biological carbon pump. Total mass flux and the fluxes of its primary components—particulate organic carbon, calcium carbonate, opal, and lithogenic matter—exhibited similar temporal trends, with three conspicuous high‐flux events. These events occurred in the summer, autumn, and winter, attributable to upwelling, aerosol deposition, and the northeast monsoon, respectively. Together, these events accounted for only 40% of the total time but approximately 80% of the 10‐month total mass flux (21% during the upwelling event, 23% during the aerosol event, and 36% during the northeast monsoon event). Each event contributed its own unique biogeochemical overprint. For example, Calcareous phytoplankton benefited from both the upwelling and aerosol deposition events, but siliceous phytoplankton benefited more than calcifiers during the upwelling conditions. The biogenic sinking particles were primarily marine authigenic, while the lithogenic matter was mainly resuspended sediment from the neighboring slope. The high flux of lithogenic matter was due to scavenging by sinking organic matter and the ballasting effect, especially during the high‐flux periods. This study illustrates that episodic intraseasonal physical processes are as important as the most common major seasonal event—the northeast monsoon—in modulating the strength of the South China Sea biological carbon pump.

The seasonal mean and synoptic fluctuation of the wintertime Taiwan Warm Current (TWC) were investigated using a well-validated finite volume community ocean model. The spatial distribution and dynamics of the synoptic fluctuation were highlighted. The seasonal mean of the wintertime TWC has two branches: an inshore branch between the 30 and 100 m isobaths and an offshore branch between the 100 and 200 m isobaths. The Coriolis term is much larger than the inertia term and is almost balanced by the pressure gradient term in both branches, indicating geostrophic balance of the mean current. Two areas with significant fluctuations of the TWC were identified during wintertime. One of the areas is located to the north of Taiwan with velocities varying in the cross-shore direction. These significant cross-shore fluctuations are driven by barotropic pressure gradients associated with the intrusion of the Taiwan Strait Current (TSC). When a strong TSC intrudes to the north of Taiwan, the isobaric slope tilts downward from south to north, leading to a cross-shore current from the coastal area to the offshore area. When the TSC intrusion is weak, the cross-shore current to the north of Taiwan is directed from offshore to inshore. The other area of significant fluctuation is located in the inshore area between the 30 and 100 m isobaths. The fluctuations are generally strong both in the alongshore and cross-shore directions, in particular at the latitudes 26.5 and 28° N. Wind affects the synoptic fluctuation through episodic events. When the northeasterly monsoon prevails, the southwestward Zhe-Min coastal current dominates the inshore area associated with a deepening of the mixed layer. When the winter monsoon is weakened or the southwesterly wind prevails, the northeastward TWC dominates in the inshore area.

The filamentous Trichodesmium and Richelia/Calothrix appear to be crucial N₂‐fixing cyanobacteria throughout the warm oligotrophic ocean, particularly in western boundary currents. The Kuroshio, the hotspot of N₂ fixation in the Pacific Ocean, intrudes into the East China Sea (ECS) and southern Yellow Sea (SYS), which may profoundly influence composition and distribution of filamentous diazotrophs. We provide high spatial resolution dataset of filamentous diazotrophs in the ECS and SYS in July and August 2013. Results showed that Trichodesmium colonies and Richelia/Calothrix were strictly restricted to warm, saline, nitrogen‐limited waters of the ECS influenced by Kuroshio and were not detected in the SYS. The density of Trichodesmium in the ECS and SYS was 8.48 × 10⁶ trichomes/m², and colonial trichomes accounted for 40%. In addition to free filaments, Richelia/Calothrix were found to be symbiotic with diatoms Hemiaulus, Rhizosolenia/Guinardia, Chaetoceros, and Bacteriastrum with a total density at 2.13 × 10⁶ heterocysts/m² in the ECS. The densities of filamentous diazotrophs were significantly higher in high‐salinity region of the ECS (mainly controlled by Kuroshio) than in low‐salinity region of the ECS and in the SYS. The densities of Trichodesmium and Richelia/Calothrix were significantly and positively correlated with temperature, salinity, and mixed‐layer depth but were negatively correlated with NO₃, turbidity, and chlorophyll‐a. These results suggested that composition and distribution of filamentous diazotrophs in the ECS and SYS were largely shaped by Kuroshio and associated physicochemical properties. We hypothesize that active N₂ fixation in Kuroshio may be substantially supported by Richelia/Calothrix in addition to Trichodesmium.