Sediment dredging is an important countermeasure for remediating eutrophic shallow lakes, which may significantly alter benthic fauna via changing sediment characteristics and bottom dissolved oxygen (DO) conditions. However, current understanding on the effects of sediment dredging on bivalves remains unclear. Here, Corbicula fluminea, a native species in Asia undergoing substantial population declines in shallow lakes in the Yangtze River Basin (China) due to eutrophication, was taken as an example to examine the response of freshwater bivalves to dredging. We hypothesized that (1) in hypoxia conditions, sediment dredging benefits the survival of C. fluminea via coarsening the sediment, which would improve DO conditions at sediment-water interface (SWI); and (2) in habitats with sufficient DO, a mixture of coarse sand and fine sediment simulating sediment conditions after dredging, would increase C. fluminea growth since this species is both filter and deposit feeder. To test the above hypotheses, we conducted an outdoor mesocosm experiment that simulated the living conditions of C. fluminea under different dissolved oxygen and sediment type conditions. In addition, we used a 15-year monitoring program of C. fluminea in Lake Taihu that have been experiencing dredging several times to assess possible changes in population dynamics. We found that coarse sediment benefited C. fluminea via improving DO conditions at SWI, indicating that dredging benefits the survival of C. fluminea, which is consistent with our first hypothesis. In sufficient DO conditions, coarse sediment improved growth of C. fluminea, consistent with our second hypothesis. However, in natural ecosystems the effectiveness of sediment dredging is time-limited. Therefore, our results also suggested that sediment dredging should be taken together with other measures, such as pollution reduction and ecological restoration, to recover C. fluminea populations.