The coastal environment of the Changjiang delta has been influenced by recent anthropogenic activities such as dam construction and increased sewage and fertilizer inputs. Previous work examined the compositional shift of marine plankton to assess ecological impacts of these activities on marine ecosystems in the Changjiang discharge area. Here we used benthic marine ostracodes collected in the Changjiang estuary and the adjacent East China Sea in the 1980s and the 2010s, respectively, to investigate temporal changes of the benthic community and controlling factors for the benthic fauna. Our results revealed more shoreward distribution of some well-known offshore ostracode species in the 2010s compared with the 1980s and a relatively more important role for environmental processes (e.g., bottom-water temperature, bottom-water salinity, and eutrophic conditions of surface water) than spatial processes (e.g., the flow of ocean currents) in structuring ostracode compositions. The temporal changes in the ostracode community are likely attributable to the combined effects of reduced fresh water and sediment discharge and eutrophic conditions of the Changjiang due to the many dams constructed along the Changjiang and population expansion in the Changjiang Basin. Results of redundancy analysis and variation partitioning suggest that ocean currents facilitated environmental filtering of ostracode species such that they could disperse to preferred environmental conditions. These findings highlight the potential uses of marine microfossils to better understand ecological impacts on benthic ecosystems in vulnerable Asian mega-deltas and provide insights into the integration of metacommunity concepts in disentangling dynamics of marine benthic communities.