The tropical South China Sea is generally warm, stratified, and nutrient-poor, with microbial communities playing a major role in pelagic carbon cycling. Using anchored observations around Dongsha Atoll and at the SouthEast Asian Time-Series Station, we examined how physical processes regulate heterotrophic bacteria and picophytoplankton across timescales ranging from hours to seasons.

Elevation-type internal solitary waves transported nutrient-rich subsurface waters into the euphotic zone and markedly stimulated bacterial activity. Maximum bacterial production and specific growth rates in wave-affected areas were approximately fivefold higher than those at control sites. Contrasting observations during different tidal phases further suggested that bacterial activity may vary with the lunar fortnightly cycle.

Eight seasonal diel surveys also revealed distinct temporal and vertical patterns among picoplankton groups. During warm, stratified periods, Prochlorococcus and picoeukaryotes formed subsurface abundance maxima, whereas Synechococcus and heterotrophic bacteria remained more abundant near the surface. Winter mixing disrupted water-column stratification, eliminated the subsurface maxima, and redistributed picoplankton toward the surface. Clear diel cycles were detected only during some surveys, with picoeukaryotes generally peaking in the early evening and Synechococcus and Prochlorococcus reaching maxima later at night. Across the eight surveys, changes in mixed-layer depth explained approximately 73% of the diel-to-seasonal variation in euphotic-zone-integrated picophytoplankton biomass, highlighting nutrient supply through vertical mixing as a major control.

These findings demonstrate that short-term nutrient pulses and seasonal changes in stratification jointly regulate microbial distribution, growth, and carbon cycling in the tropical South China Sea.