Intensive aquaculture has been a major source of coastal pollution. Microorganisms play a critical role in primary production and biogeochemical processes such as substance cycling and energy transformation in coastal ecosystems. Bacterioplankton are considered to be a dominant group because of their many contributions to ecosystem functional processes. Studying the influences of aquaculture activities on bacterial diversity in water is significant for assessing the structure and function of mariculture ecosystems. Xiangshan Bay, an important mariculture base located in Ningbo, China, is subject to a large influx of organic matter from the rapid development of aquaculture. Thus, understanding the responsive pattern of the bacterioplankton community to aquaculture sheds light on indicating and evaluating the health status of the mariculture ecosystem. In this study, water samples were collected separately from three depths: the surface, middle, and bottom levels of the water column (corresponding to 0.5, 2.5, and 8.0 m below the water surface, respectively), from a cage culture area and a non-cultured area in Xiangshan Bay, on April 10, 2012. Using the 16S rRNA gene amplicon pyrosequencing technique, we evaluated the effects of aquaculture activities on variations within bacterioplankton communities. The results showed that cage aquaculture dramatically changed the geochemical variables of water. For example, there was a substantial increase of chemical oxygen demand in the culture area. In addition, cage aquaculture significantly (P < 0.05) altered the bacterioplankton community structure, although the alpha diversity was not affected. The bacterioplankton communities were very similar across the three water depths, dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Betaproteobacteria, Epsilonproteobacteria, and Unclassified Proteobacteria, accounting for 98.64% of the total bacteria. The relative abundances of some dominant phyla were considerably different between the two investigated areas. For example, the relative abundances of Bacteroidetes and Actinobacteria were significantly lower in the non-cultured area than in the cage culture area, while that of Gammaproteobacteria was significantly higher in the non-cultured area. Similarity percentage (SIMPER) analysis further indicated that the presence of Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes taxa controlled the differences in bacterial communities between the two areas, which contributed to 45.02% of the overall dissimilarity. Redundancy analysis (RDA) showed that the bacterioplankton community variation significantly correlated with chemical oxygen demand, phosphate, ammonium, and total organic carbon. Partial redundancy analysis (pRDA) was conducted in order to quantify the effect of the geographic distance between the two investigated areas on the differences between the bacteria communities. The results showed that the above-mentioned environmental factors in total contributed 38.18% of the bacteria community variation, while the geographic distance contributed only 10.66%, indicating that the influence of environmental factors on bacterial communities was much greater than that of the geographic distance. Overall, this study demonstrated that coastal aquaculture could cause eutrophication of rearing water, which, in turn, drove the variation of the bacterioplankton community, and remarkably altered the relative abundances of Bacteroidetes, Actinobacteria, and Gammaproteobacteria. The sensitivity of these bacteria to the concentration changes of pollutants, represented by nitrogen and phosphorus, indicates their potential usage in assessing the quality of aquaculture water and the health and stability of an aquaculture ecosystem.