To evaluate the effects of different anthropogenic activities on zooplankton and the pelagic ecosystem, we conducted seasonal cruises in 2010 to assess spatial heterogeneity among the mesozooplankton communities of Xiangshan Bay, a subtropical semi-enclosed bay in China. The evaluation included five different areas: a kelp farm, an oyster farm, a fish farm, the thermal discharge area of a power plant, and an artificial reef, and we aimed to identify whether anthropogenic activities dominated spatial variation in the mesozooplankton communities. The results demonstrated clear spatial heterogeneity among the mesozooplankton communities of the studied areas, dominantly driven by natural hydrographic properties, except in the area near the thermal discharge outlet of the power station. In the outlet area, thermal shock caused by the discharge influenced the mesozooplankton community by decreasing abundance and biomass throughout the four seasons, even causing a shift in the dominant species near the outlet during summer from Acartia pacifica to eurythermal and warm water taxa. Unique features of the mesozooplankton community in the oyster farm may be due to the combined effects of oyster culture and the natural environment in the branch harbour. However, kelp and fish culture, and the construction of an artificial reef did not exert any obvious influence on the mesozooplankton communities up to 2010, probably because of the small scale of the aquaculture and a time lag in the rehabilitation effects of the artificial reef. Thus, our results suggested that the dominant factors influencing spatial variations of mesozooplankton communities in Xiangshan Bay were still the natural hydrographic properties, but the thermal discharge was an anthropogenic activity that changed the pelagic ecosystem, and should be supervised.