Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.