Abstract: Based on the MODIS/AQUA images of Shenzhen coastal waters and the VGPM model modified by the estimation of chlorophyll a with the in situ buoy data, the temporal and spatial distribution of net primary productivity is studied. The results shows that the net primary productivity (NPP) decreased toward the offshore waters in February, May, August and October with higher NPP in the east and lower in the west. The seasonal fluctuation is not evident. Moreover, the chlorophyll a concentration in 4 areas varied consistently with seasons and it is the highest in summer and slightly lower in autumn and winter. The impacting factors varied with the areas, where the Pearl River Estuary was affected by the phytoplankton species and density due to the monsoon, Daya Bay was mainly controlled by nutrients, Dapeng Bay was impacted by the seasonal variations of residual current and Shenzhen Bay was mostly related to the seasonal change of phytoplankton density. In addition, we found that the NPP of Pearl River Estuary were characterized by a seasonal pattern, with the highest in spring and summer and the lowest in autumn and winter. The NPP of Dapeng Bay were highest in summer and the seasonal fluctuation tended to be the same with the chlorophyll a concentration. The NPP of Shenzhen Bay were highest in summer and the pattern of seasonal fluctuation tend to be the same with the sea surface temperature. The NPP of Daya Bay fluctuated markedly with seasons and it was the highest in summer and winter and the lowest in spring and autumn.