Denitrification is a key process in global nitrogen cycling, yet its microbial mechanisms in arid and semi-arid freshwater systems remain insufficiently understood. Previous studies have focused on eutrophic lakes and wetlands, overlooking small, semi-closed water bodies where fluctuating hydrology and nutrient scarcity strongly influence microbial activity. To address this gap, we investigated nirK-type denitrifying bacterial communities in rainwater harvesting cellars (RWHC) on the Loess Plateau of Northwest China. High-throughput sequencing and multivariate analyses were used to characterize the nirK-type denitrifier community composition and environmental drivers. Results showed that nirK-bearing Alphaproteobacteria, mainly Bradyrhizobium, Paracoccus, and Rubellimicrobium, dominated the assemblages. Total phosphorus, nitrate, and pH were key positive factors shaping community structure, while ammonium and organic matter load exerted negative constraints. Path modeling quantified that environmental factors influenced denitrification potential through both a significant direct effect and a stronger indirect effect mediated by shifts in taxonomic composition, with core taxa such as Paracoccus and Rubellimicrobium exerting the strongest direct effects on functional gene abundance. This study provides the first integrated ecological insight into nirK denitrifiers in RWHC, demonstrating that microbial identity, rather than diversity alone, governs nitrogen transformation outcomes. The co-occurrence of taxa with complete and partial denitrification pathways highlights a dynamic balance between nitrogen removal and N2O emission potential. These findings establish a theoretical framework for predicting microbial functional potential in small-scale water infrastructures under environmental change.