Water and sediment regulation involves artificially depositing sediments from rivers and reservoirs to the sea, thus increasing the main channel discharge capacity. Based on survey data before and after water and sediment regulation (June and July) in the Yellow River during 2011-2013, we used the index of relative importance (IRI), ANOVA, and multivariate analysis to evaluate the effect of this regulation procedure on fishery resources (species composition, distribution, and dominance) in the Yellow River estuary. We identified 92 species, including 52 fish species. Palaemon gravieri were dominant species, although their exact ranking varied across years. From 2011 to 2013, biomass first increased, then decreased, whereas fishery resources clearly changed in structure before and after water and sediment regulation. Average fishery resource density increased after water discharge and was low near the river mouth. CLUSTER analysis showed that between-year variation in community structure was the greatest, followed by variation resulting from water and sediment regulation, and finally, by variation between sampling sections. Post-regulation changes in water input and nutrient concentration of the Yellow River likely contribute to the variation in species composition and distribution in the region.