Estuarine ecosystem structures and functions are subjected to environmental perturbations from natural processes and anthropogenic activities. Although the fundamental contribution of bacterioplanktonic communities to sustainability and services of estuarine ecosystems is widely investigated, it remains unclear which environmental factors govern community and how bacterioplanktonic communities respond to environmental perturbations in estuarine ecosystems. Here we examined the bacterioplanktonic communities of 144 surface water samples collected for three years from the subtropical Pearl River Estuary, China, using 16S rRNA full-length gene amplicons sequencing with PacBio platform.