In marine ecosystems, the distribution pattern and abundance of bacterioplankton are directly related to environmental conditions. In order to study the effect of environmental factors on bacterial abundance, surface water samples were collected in March, May, August, and October 2015 from three coastal regions namely, the Pearl River Estuary, Shenzhen Bay and Daya Bay in Shenzhen, China. The abundance of bacterioplankton, bacteria with high DNA content (HNA subgroup bacteria) and bacteria with low DNA content (LNA subgroup bacteria) in the coastal waters of Shenzhen were measured by flow cytometry to analyze their temporal and spatial distribution pattern and to explore their responses to environmental factors. The results showed that the average abundance of bacterioplankton in Shenzhen Bay (7.67×10⁶ cells/mL), the Pearl River Estuary (3.82×10⁶ cells/mL), and Daya Bay (3.38×10⁶ cells/mL) had a decreasing trend. The abundance of bacterioplankton in the Pearl River Estuary increased from far coast to near coast sites; however, there were no significant differences in abundance among the sites in Shenzhen Bay (P > 0.05) and Daya Bay (P > 0.05). The temporal variation in bacterioplankton abundance in the three regions was mainly affected by temperature, whereas spatial variation was predominantly controlled by the concentration of chlorophyll a and nutrient matter, such as nitrogen and phosphorus. Additionally, the temporal and spatial variability of HNA subgroup bacterial abundance was greater than that of LNA subgroup bacteria (P < 0.01). The HNA subgroup bacteria was significantly affected by temperature (P < 0.01) whereas LNA subgroup bacteria were not (P > 0.05). The different responses of HNA and LNA subgroup bacteria to certain environmental factors imply that they play partially overlapping but slightly different roles in the coastal ecosystem.