Ammonium nitrogen (NHx) in atmospheric wet deposition is a primary external nitrogen source for reservoir-type water sources, and identifying its sources is crucial for controlling nitrogen pollution in water. This study aimed to examine the NHx characteristics and sources in wet deposition in the Xichuan reservoir area of the Danjiangkou Reservoir, the South-to-North Water Diversion Project (SNWDP) water source, from September 2019 to August 2020. Major inorganic nitrogen concentrations in precipitation and ammonia-nitrogen isotope (δ15N–NH4+) values were measured, and the sources were analyzed using the Bayesian mixing model. The results showed that NH4+ was the main inorganic nitrogen form in wet deposition, with a concentration ranged of 0.16–5.26 mg L−1. The δ15N–NH4+ values ranged from −14.7‰ to +6.3‰, with significant isotopic effects from agricultural sources and climatic conditions, showing higher values in summer and lower values in winter. The release of ammonia (NH3) from agricultural sources was the primary NHx source (58.0%–76.6%), with fertilizer application being the most significant contributor (32.1%–46.6%). Seasonally, the relative contribution of agricultural sources to NH4+ in wet deposition was higher in autumn and winter. Spatially, agricultural activities significantly impacted atmospheric nitrogen accumulation across the reservoir area. This study quantified NHx sources in wet deposition, providing isotopic evidence and scientific references for nitrogen control measures and atmospheric nitrogen cycling studies.