To explore the effects of three different aquacultures on planktonic ecosystem in semi-closed bay, the macro- and meso-zooplankton community, meso- and micro-zooplankton community and 12 kinds of associated environmental factors were studied inside and outside the fish cage aquaculture, kelp raft aquaculture, and farms in Xiangshan Bay via seasonal cruises during 2015. The results demonstrate that: compared with the control areas in the oyster farm, the macro- and meso-zooplankton community composition changed obviously, and the dominance of Acartia pacifica declined during summer and autumn, while that of Centropages abdominalis went up in winter; in the fish farm, the dominant species of macro- and meso-zooplankton changed, with the dominance of Centropages abdominalis declining during spring and winter, and dominant species composition changing obviously in autumn; however, in the kelp farm, there was no marked change in zooplankton community; moreover, the effects of the three different aquacultures on biomass, abundance and α-diversity of zooplankton community were nonsignificant. Analyzing the above results, combined with the hydrological characteristics in Xiangshan Bay and the environmental factors inside and outside the farms, we considered, the change in zooplankton community was a comprehensive result of oyster filter-feeding behavior and the poor water exchange capacity in Tie Harbor, and the zooplankton dominant species variation might relate to elevated total phosphorus content in the farm; in our study, fish cage aquaculture effects on environment and zooplankton were less, mainly due to the small aquaculture scale recently and good hydrodynamic condition in Xihu Harbor; the kelp aquaculture was inadequate to influence the water quality and zooplankton community, because of its small cultural scale and short cultural period every year (only in spring and winter). In addition, the variation in macro- and meso-zooplankton was more obvious than that in meso- and micro-zooplankton, which may be related to the higher stability in meso- and micro-zooplankton community.