Species constitutions, components of dominant species and biodiversity of macrobenthos in the Yellow River Estuary at 18 sampling locations were investigated, to compare the macrobenthos alterations during the water and sediment discharge regulation (WSDR) project period. A total of ten water environmental variables were analyzed by factor analysis, and the redundancy of the main water environmental variables and parameters of macrobenthos community were also investigated. The results showed that a total of 118 species were identified, and there were no differences of species constitutions during the WSDR project period. The biomass of each investigation was (4.31±1.43), (5.57±3.85) and (4.04±1.38)g/m2. The abundance was (241±59), (173±44) and (199±40)ind/m2respectively. The dominant species was Moerella jedoensis, which was not different among the earlier, middle and later stage of the WSDR project in 2013. Diversity index analysis showed that water quality was good before and after the WSDR in the Yellow River. The BOPA (benthic opportunistic polychaetes amphipods) index, appropriate for surveying the temporal changes of macrobenthic systems at high frequencies, can be used to differentiate estuarine and coastal communities into five statuses of ecological quality. The trend revealed by the BOPA index and statistical analysis of environmental variables suggested that the Yellow River Estuary was under ecologically healthy condition during the WSDR project period, except the mouth region. Analysis of the correlations among 41 species of macrobenthos and environmental factors during the WSDR project period showed that environmental factors such as water depth, pH, salinity and dissolved oxygen played a significant role in affecting the macrobenthic community structure. The WSDR project affected the northeast and estuary region, resulting in the death of mollusks and greatly increasing opportunistic polychaetes. Therefore, all the results indicated that there were certain negative effects on macrobenthos during the WSDR project period. ©, 2015, Editorial department of Molecular Catalysis. All right reserved.