Abstract: In recent years, the water quality of the Daliao River is becoming more and more seriously polluted by nitrogen with the economic development on both sides of the Loaohe estuary. Denitrification is an important process in the nitrogen cycle mediated by microorganisms, which is of great significance to the removal of excess nitrogen in the estuary water and the alleviation of eutrophication. So, it is particularly important to conduct a research on the denitrification in the Daliao River estuary and its adjacent areas. This paper takes the Daliao River Basin, estuary and coastal waters as the research object, uses real-time quantitative PCR to analyze the spatial distribution characteristics of denitrifying bacteria (mainly functional genes nirS, nirK and nosZ) in the water, and study the correlation between environmental factors and gene abundance by factor analysis and redundancy analysis (RDA). The results show that: (1) The variation ranges of nirK, nirS and nosZ genes in water samples are 7.73×10⁵-2.54×10⁸ copies/L, 3.19×10⁵-3.19×10⁷ copies/L, 3.22×10³-4.92×10⁵ copies/L, respectively. The average value of the three genes is in descending order nirK > nirS > nosZ. Among the three genes, most of the nirK and nirS genes have higher concentrations in the upper reaches of the investigated rivers and at the estuary sites, while the abundance of nosZ genes gradually increases from the upstream station to the estuary station in the river section, and decreases from the estuary to the coastal waters. (2) The (nirK+nirS)/nosZ of the Daliao River Estuary and its adjacent areas are between 3.23×10¹-1.76×10³, with an average value of 454.77, indicating that there are more N₂O gas emissions, especially from the estuary to the offshore area. (3) As, Cd, Cr, SiO₃^2-, NO₃^-, T, pH and salinity dominate the overall condition of the water environment in the Daliao River Estuary and adjacent areas. The correlation of the influence of water environmental factors on the abundance of denitrification functional genes is ρ(DO) > ρ(TN) > ρ(NO₂^-) > ρ(SiO₃^2-) > ρ(Cd) > ρ(NO₃^-) > salt > ρ(As) > ρ(Cr) > T > ρ(Zn) > pH. Monte Carlo test shows that there is no significant influence factors. Therefore, the abundance of denitrification functional genes in the Daliao River Estuary and adjacent areas is the result of the interaction and joint influence of various environmental factors. In summary, the above studies show that microorganisms related to denitrification in water have different responses to the environment, and various environmental factors jointly control the community composition. In order to better manage and protect the water bodies, continuous attention should be paid to denitrification functional genes in water bodies.