Plateau lakes are typically dystrophic and are sensitive to small changes in nutrient deposition. With this assumption, we investigated the concentrations, fluxes, and sources of nitrogen (N) and phosphorus (P) in the atmospheric wet deposition (AWD) of the Lake Qinghai Watershed (LQW), which is the largest inland lake in China, for one year from October 2017 to September 2018. The results showed that the annual volume-weighted mean (VWM) concentrations (mg L−1) in the AWD were 1.97 for NH4+-N, 0.55 for NO3−-N, 0.04 for NO2−-N, 0.77 for dissolved organic N (DON), 3.33 for total dissolved N (TDN), 0.30 for dissolved inorganic P (DIP), 0.07 for dissolved organic P (DOP), 0.36 for total dissolved P (TDP), and 0.99 for reactive sulfur (SO42−-S). The annual AWD fluxes of TDN and TDP were 16.82 and 1.86 kg ha−1 yr−1, respectively. Strong dilution effects in the wet season, a long residency time of nutrient-rich aerosols in the dry season, strong ammonia volatilization in the wet and warm seasons, and moisture sources dominated the seasonal or monthly changing characteristics of N and P concentrations in the AWD, including high in the wet season and low in the dry season for NH4+-N, low in the wet season and high in the dry season for NO3−-N, and generally increasing from April to September for DIP and DOP. Precipitation quantity dominated the monthly changes in the N and P fluxes of the AWD, which gradually increased from April to August and then decreased in September. N and P in the AWD mostly originated from anthropogenic sources. High ammonia volatilization from local intense animal husbandry, alkaline soils and lakes led to a relatively high NH4+-N concentration compared with other sites of the Qinghai-Tibet Plateau, China, and in the world. The N/P molar ratio in the precipitation was higher than 16, which might have effect on the aquatic ecosystems of Lake Qinghai. Ammonia volatilization fluxes and atmospheric dry deposition fluxes of N and P should be further studied to completely understand the geochemical cycles of N and P in the LQW.