Nitrogen (N) deposition plays a key role in ecosystem function as one of the major N sources for natural vegetation, particularly in karst agricultural areas with thin soil cover, which drive the karst N fate via rainwater. To understand the seasonal and spatial variation in nitrogen deposition and to identify the major sources of nitrate in wet deposition in a karst agricultural area (Houzhai Catchment) in southwestern China, two sites with different land use were selected to assess wet and dry deposition for one year. Houzhai village (HZV) is an area highly influenced by agriculture, whereas Muzhu reservoir (MZR) is a more pristine environment with less anthropogenic influence. Nitrogenous species and dual nitrate isotopes were analyzed. The results showed that agriculture-derived NH4+ was the major contributor of annual total wet N deposition ( > 55 %). The contribution of NH4+ to wet N deposition was 1.63 times higher than that of NO(3)(- )and dissolved organic nitrogen (DON). The annual nitrogen deposition in this study was approximately twice as much as the average wet N deposition over China, while lower dry N deposition relative to other Chinese monitoring sites was observed. The delta N-15-NO3- showed a seasonal trend of negative summer values and positive winter values, which were primarily controlled by the variations in NOx emission sources. Seasonal variation in delta O-18-NO3- was mainly controlled by NO, oxidation pathways and showed a similar trend to delta N-15-NO3-. The contributions from four endmembers (coal combustion, vehicle exhaust, biomass burning, and soil emission) were calculated using a stable isotope mixing model. Contributions show a clear seasonal variation (except vehicle exhaust), with the four sources accounting for 20.0 %, 25.6 %, 22.9 % and 31.5 % respectively (annual mean probability estimate, AMPE) at HZV, and 19.0 %, 27.8 %, 23.2 % and 30.0 % (AMPE) at MZR. Isotopic evidence determined agricultural soil emission is a major contributor to rainwater during the summer growing season, which can significantly impact the agricultural ecosystems.