Denitrification community in wetland plays an important role in nitrogen removal. The present study investigated the seasonal and spatial dynamics of denitrification rate and nirS-denitrifier communities and the potential influential factors in a large wetland system treating polluted river water. Wetland denitrification rate and the abundance, richness, diversity and composition of nirS-denitrifier community were found to vary with season and sampling site. Both wetland denitrification rate and denitrifier community were related to plant type. Wetland soils and sediments differed greatly in either denitrification rate or denitrifier community structure. Wetland generally had lower denitrification rate and denitrifier abundance in summer than in spring and winter. Denitrification rate showed no direct correlation to denitrifier abundance but was positively correlated to denitrifier diversity. Denitrification rate could be mediated by denitrifier community structure. Moreover, Spearman rank correlation analysis suggested that denitrification rate was significantly correlated to sediment/soil ammonia, nitrate, nitrite, total phosphorus and pH, while denitrifier abundance was significantly correlated to total phosphorus and temperature. Nitrite, total nitrogen, total organic carbon, and the ratio of total organic carbon to total nitrogen showed significant correlations with wetland denitrifier diversity, while ammonia, nitrate, total nitrogen and total phosphorus might have important roles in shaping wetland denitrifier community structure. In addition, for each wetland sediment or soil, 0.8–46.2% of the retrieved nirS sequences could be related to the sequences from cultivated denitrifiers. Dechloromonas-like denitrifiers were more abundant in wetland sediments than in wetland soils.