Nitrogen deposition is an important means of exogenous nitrogen input in reservoir water. Agricultural activities around the reservoir lead to a sharp increase in the concentration of ammonia in the atmosphere, which poses a threat to the reservoir water body. Clarifying the contribution of agricultural ammonia release to atmospheric NHx (gaseous NH3 and particulate NH4+), in the reservoir area can provide a theoretical foundation for local reactive nitrogen control. We collected atmospheric NH3 and NH4+ samples during the agricultural periods and analyzed the isotopic characteristics of atmospheric NHx and the contribution rates of different ammonia sources in the Xichuan area of the Danjiangkou Reservoir. The results showed that the initial δ15N values of NH3 (–30.0‰ to –7.2‰) and particulate NH4+(–33‰ to +4.9‰ for finer and coarser particles, respectively) are different, and their contribution ratios from dissimilar ammonia sources are also different, among which NH4+ is more susceptible to meteorological factors. However, since the atmospheric NHx in the Xichuan area is mainly gaseous NH3, the final sources of atmospheric ammonia nitrogen source depend on gaseous NH3. Agricultural sources (59%-74%) were the main NH3 sources in this area. Among them, the fertilizer use emission was dominant; it had the highest contribution rate in summer during the agricultural period and a more prominent impact in areas with less human interference. Reasonable regulation of the application of high-ammonia releasing fertilizer, especially during the agricultural period in summer, is an effective way to reduce the threat of atmospheric ammonia to water health.