[Objective] The water quality of Bohai Sea was monitored from 2015 to 2020, and the correlation between the change of ecological environment in the coastal waters of the Yellow River estuary and sediment and runoff into the sea was analyzed, in order to provide a basis for the ecological environment protection in the Yellow River estuary.[Methods] The water quality pollution index and biodiversity index evaluation method were used to analyze and evaluate the Pearson correlation coefficients between marine biodiversity and each monitoring index of seawater using SPSS software.[Results] The main pollutant exceeding the standard in the coastal waters of the Yellow River estuary was inorganic nitrogen, and its single pollution index fluctuated from 0.63 to 1.40, which exceeded the second-class water quality standard. The concentration of inorganic nitrogen was positively correlated with the sediment transport from the Yellow River to the sea, and the correlation coefficient was 0.833 (p<0.01). During the summer survey, 77 species of phytoplankton were collected, mainly located in the northern waters of the Yellow River estuary. Since 2018, the number of phytoplankton species has shown a downward trend, from 67 species in 2015 to 42 species in 2020; 52 species of zooplankton were collected, mainly Located in the offshore waters of the northeast of the estuary, the species of zooplankton have gradually increased since 2015, and the diversity index has risen from the level Ⅳ in 2015 to the level Ⅲ in 2020; 92 species of macrobenthos were collected, mainly located in the east of the estuary In the offshore waters, the species and density of benthic species have increased since 2018. The diversity index has increased from 2.18 in 2018 to 3.01 in 2020.[Conclusion] Since 2015, the water quality in the coastal waters of the Yellow River Estuary meets the water quality requirements for industrial water areas and coastal scenic tourist areas in Sea Water Quality Standard (GB 3097-1997), and the ecological situation has gradually improved. There was a significant positive correlation between the zooplankton diversity index in the coastal waters of the Yellow River estuary and the sediment transport and runoff of the Yellow River, with correlation coefficients of 0.941 (p<0.01) and 0.918 (p<0.01), respectively. There was no significant correlation between phytoplankton and benthic biodiversity indices and sediment runoff.