Recent research has greatly expanded our understanding of microbial metacommunities in aquatic ecosystems. However, patterns at the mesoscale are still poorly understood. We present the first simultaneous analyses of the biogeography and co-occurrence patterns of generalists and specialists marine bacteria from three subtropical bays of China and test for signals of ecological processes (i.e., stochastic and deterministic processes) in biogeography and community assembly. Results showed that compared to specialists, bacterial generalists were less diverse, and were more widely dispersed in the three subtropical bays. Network analysis indicated that both habitat generalists and specialists showed non-random co-occurrence patterns, and specialists had a more complex co-occurrence pattern than generalists. Further, specialists co-occurrence network exhibited distinct robust structure compared to generalists, indicating that the both taxa showed different network stability. Our null models indicated that the generalists and specialists were primarily shaped by deterministic processes - such as variable selection. However, deterministic processes played a greater role in the community variation of specialists (84%) than generalists (56%). The study has broadened our understanding of generalists and specialists distribution in the bacterioplankton; further revealing the dominant roles of similar ecological mechanisms (deterministic processes) in shaping the community assembly. The differences in complex and stable co-occurrence pattern between generalists and specialists could be driven by deterministic processes. By considering the roles of species traits and ecological processes, we provide a deeper mechanistic understanding of bacterial biogeographical and co-existence patterns.