Purpose Dissimilatory nitrate (NO3-) reduction to ammonium (DNRA) is a significant nitrogen (N) transformation process in estuarine ecosystem. The objectives of this study were to clarify the key biotic and abiotic factors influencing DNRA potential rates in Xiamen Bay. Methods We characterized DNRA, anammox, and denitrification rates through (15) N isotope tracer experiments. Then quantitative real-time PCR and high-throughput sequencing analysis were conducted to analyze the abundance and community of DNRA bacteria. Spearman correlation analysis was used to understand the relationships of DNRA rate, nrfA abundance, and community with environmental characteristics. Results Denitrification was dominated in dissimilatory NO3- reduction processes in sediments of Xiamen Bay. Bacteroidetes and Proteobacteria were the main phyla of DNRA bacteria and Pelobacter was the dominant genus. Spearman correlation analysis showed that DNRA rate was significantly positively correlated with nitrite (NO2-) and NO3- in interstitial water, total organic carbon (TOC), acid volatile sulfide (AVS), and total nitrogen (TN) in sediment. Besides, nrfA abundance showed positive correlations with DNRA rate, NO2-, TOC, AVS, and TN. Furthermore, AVS and nrfA abundance were positively correlated with Pelobacter. Conclusion DNRA rates were limited by sulfide, organic carbon, abundances of nrfA gene, and DNRA bacteria. Sulfide and organic carbon shaped DNRA bacterial community thereby controlled DNRA rate. Heterotrophic sulfide-producing genus (Pelobacter) prevailed among DNRA bacteria, which might support autotrophic DNRA bacteria. In this way, heterotrophic and autotrophic DNRA bacteria were connected through sulfide-producing genus and acted as a whole functional community.