Data on the macrobenthos, bottom seawater, and sediment from 26 sampling stations in the Huanghe River estuary and adjacent seas in China, were collected in June 2020. Community structure, species diversity, taxonomic diversity of the macrobenthos, and the relationships of these variables with environmental factors were analyzed. The funnels and contours of average taxonomic distinctness (Δ+) and variation in taxonomic distinctness (Λ+) were used to indicate the disturbance status of the estuary seas. These findings revealed differences in macrobenthic community structure and biodiversity between the estuary and the adjacent seas. A total of 88 macrobenthic species were collected in the Huanghe River estuary and its adjacent seas. Abundances in the estuary, Section C, and Section D were 60 ind. m−2, 183 ind. m−2, and 320 ind. m−2, respectively, The biomass in the estuary, Section C, and Section D was 6.74 g·m−2, 15.72 g·m−2, and 9.07 g·m−2, respectively. There were significant differences in the number of species and their abundances between the estuary and adjacent seas (p < 0.01). Glycinde bonhourei, Sternaspis scutata, Moerella hilaris, Liljeborgia serrata, Iphinoe tenera, and Lineus sp. were the dominant species. The community dissimilarity of the estuary and adjacent seas reached >79.66% (p = 0.001). The results of k-means clustering analysis showed that the macrobenthic community could be divided into three types. High Margalef richness index (d) and Shannon–Wiener diversity index (H′) values were observed in the northern portion of the estuary and the seas in Laizhou Bay. The theoretical mean values of Δ+ and Λ+ were 90.8 and 267.7, respectively. High values of Δ+ were observed in Section A2-B2-C2-D2 where the communities were distantly related. Low values were observed in Laizhou Bay. The distribution of Λ+ was the complete opposite of that of Δ+. Deviations in the 95% confidence interval were observed at five stations (A2, A3, B1, B2, and D2). The northern sea of the Huanghe River estuary was disturbed. Spearman correlation analysis showed that ∆ was positively correlated with total organic carbon, heavy metals, fine silt, and clay. Heavy metal and TOC in the Huanghe River estuary and adjacent seas may be positively correlated with the reproduction of opportunistic species.
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