Objective Coastal wetlands are important natural sources of nitrous oxide (N₂O), and the distribution of denitrification genes nirS and nirK directly influences their N₂O emission potential. Vegetation types can significantly regulate the abundance of these genes by altering soil physicochemical properties and carbon-nitrogen availability, while the underlying mechanisms remain unclear. Methods Soils were collected from five representative habitats—Kandelia obovata (mangrove), Spartina alterniflora, Cyperus malaccensis, Phragmites australis, and unvegetated mudflat—in the Minjiang River estuary wetland at depths of 0-10, 10-20, and 20-30 cm. The abundance of nirS and nirK was quantified by real-time quantitative PCR, and their environmental drivers were analyzed through random forest modeling and correlation analysis. Results The abundance of nirS and nirK in all the vegetated soils was significantly higher than that in the unvegetated mudflat, with the highest values observed in the surface soil (0-10 cm) under P. australis. Both genes showed significantly decreased abundance as the soil depth increased, presenting a distinct surface enrichment effect. The nirS/nirK ratio was greater than 5 across all soil samples, indicating the dominance of nirS-type denitrifiers. The mangrove surface soil exhibited the highest nirS/nirK ratio, likely due to low dissolved organic carbon (DOC) levels limiting nirK-type denitrifiers. Random forest analysis identified soil electrical conductivity as the primary driver of nirS and nirK abundance, while available phosphorus (AP) was the dominant factor influencing the nirS/nirK ratio. High salinity promoted the enrichment of both genes, whereas high AP concentrations increased the nirS/nirK ratio. Conclusion Vegetation type and soil depth jointly shape the distribution patterns of nitrite reductase genes in the Minjiang River estuary wetland by regulating soil salinity, DOC, and nutrient availability. The results provide insights for nitrogen cycle management in coastal wetlands.