To determine if water-sediment regulation has affected macrobenthic community structure in the Huanghe River Estuary, China, macrobenthic samples were collected following regulation events from 2012 to 2016. We identify seven phyla and 138 macrobenthic species from within samples throughout the survey area, over time. Species richness and abundance in 2012 were significantly higher than in 2016. Biomass did not differ significantly during 2012–2016. Dominant species were mostly small polychaetes, with mollusks, arthropods, and echinoderms all being relatively rare. In 2016, dominant species were small polychaetes. MDS reveals macrobenthic communities at all surveyed distances from the estuary to have become the same community structure over time. ShannonWiener diversity and Margalef richness indexes trended down over time. CCA reveals the most dominant sediment-dwelling species to prefer lower dissolved oxygen, sulfides, and pH, and sediments with high D₅₀ and low clay content. We speculate that water-sediment regulation has affected seabed communities, particularly Region A in our survey area.