In this study, the comparative effects of the two disturbances (aquaculture and water level fluctuations) on macroinvertebrate communities were explored in two waterbodies connected with the reservoir system of Three Gorges Reservoir (TGR) in China. One water body called Gaoyang Bay which suffered organic pollution from intensive aquaculture. Another named Hanfeng Lake, where the effects of water-level fluctuations are obvious. The results showed that aquaculture could significantly affect the chemical forms of nutrients, decrease the α-diversity and increase the β-diversity of macroinvertebrates although the communities in the treatment area in Gaoyang Bay were not fundamentally changed comparing to the control area in the same bay. The densities of macroinvertebrates in the treatment area were significantly lower than that of the control area. The composition of functional feeding groups in the treatment area was close to that in Hanfeng Lake, but obviously different from that in the control area in Gaoyang Bay and the collectors and predators dominated the communities in this control area with the highest percentages. Although water-level fluctuations had negative effects on the communities by decreasing the α-diversity and increasing the β-diversity, which were confirmed by the values of Simpson index, Shannon-Wiener index and Harrison's index in the control area of Gaoyang bay and Hanfeng Lake, the adverse effects were relative low compared to aquaculture. In the bays of TGR, the small-scale disturbance (aquaculture activities) had more significant negative effects compared to the big-scale disturbance (water-level fluctuations related to dam operation of TGR).