The study of community assembly offers novel perspectives into the underlying mechanisms governing biodiversity shifts over space. The river-sea continuum is a unique ecosystem where microorganisms are directionally dispersed, but they also encounter selection owing to strong environmental gradients. To test the contrasting mechanisms that potentially govern the microbial metacommunity dynamics, namely homogenizing dispersal and selection, we characterized both the total and active bacterial communities in the Pearl River-South China Sea Continuum during the wet (summer) and dry (winter) seasons via high-throughput sequencing. Our results revealed that selection was more important than homogenizing dispersal in both the total and active fractions of the bacterial communities. Homogeneous selection was the most important process on average in all four cases (i.e., total and active bacterial communities in two seasons), which was mainly due to the large phylogenetic extent (associated with rarity) of bacterial communities and our fine-spatial sampling design. Moreover, the total and active communities were assembled more by homogeneous and heterogeneous selection, respectively, supporting that the total bacteria were less responsive to environmental gradients than the active bacteria. In summary, our results provide insights into the assembly of bacterial communities in natural ecosystems exhibiting strong spatial connectivity and environmental heterogeneities.