Vibrio, a bacterial genus widespread in aquatic systems that contains several pathogenic species, is known for its potential accumulation in aquacultures. Thus, release of untreated aquaculture wastewater could release high doses of such bacteria into the environment, replacing naturally occurring Vibrio populations with potentially pathogenic species. Especially in areas strongly affected by aquaculture industries, such as the island Hainan in the south of China, such a potential influence on bacterial composition poses risks for the environment and humans. To evaluate the importance of Vibrio assemblages in this region, water, sediment, seagrass and tissue samples from aquaculture and adjoining coast and river systems were analyzed using Illumina 16S rRNA gene sequencing. The results indicate that depending on the operating system of an aquaculture, different effects on Vibrio community structure and abundance can be observed. Classical pond aquaculture decreased Vibrio diversity, while relative abundances of Vibrio 16S rRNA genes were similar to those of the coastal reference populations. In comparison, aquacultures that were continuously flushed with marine water had a Vibrio community structure and diversity similar to that of the coast but with elevated levels of Vibrio sequence reads. Although an impact within the aquacultures could be seen, there was no clear evidence that aquaculture facilities altered the Vibrio composition or led to a visible increase in the relative abundance of Vibrio genes in the environment.