Coastal estuaries are increasingly impacted by anthropogenic nitrogen inputs, disrupting nitrogen cycling and posing significant threats to ecosystem health. This study investigates nitrogen sources and transformation processes in the Jiulong River Estuary (JRE), a highly eutrophic subtropical estuary in Southeast China. By analyzing and comparing samples from groundwater, surface water, and sediment, this study reveals distinct nitrogen transformation dynamics across interconnected environmental compartments. A comprehensive framework integrating stable isotope analysis, sediment incubation experiments, and microbial molecular techniques was employed to characterize nitrogen dynamics both regionally and at the sediment-water interface within diverse wetland types. Manure and sewage were identified as the primary nitrogen sources. Salinity emerged as a key regulator of nitrogen transformations, with freshwater wetlands exhibiting the highest denitrification potential, followed by mudflats, aquaculture ponds, and mangroves. Abiotic factors, including hydrological conditions and wetland types, were found to predominantly drive nitrogen transformations, while biotic factors, such as microbial community composition and functional gene abundances, played a secondary but interconnected role under the influence of abiotic drivers. These findings offer valuable insights into nitrogen cycling in estuarine ecosystems and propose a robust framework for mitigating nitrogen pollution and managing eutrophication in coastal regions.