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Abstract Dust has the potential to play a significant role in the nutrient dynamics of alpine watersheds with important ecological implications. However, little is known about how dust nutrients circulate through the environment and which watershed characteristics facilitate dust impacts on water quality. This study explored the contribution of dust‐deposited nutrients, focusing on a high‐elevation Long Term Ecological Research site, where dust samples have been continuously collected since 2017. We incorporated observed dust nutrient compositions, including fractions of inorganic and organic nitrogen and phosphorus, into a popular hydrological model, the Soil and Water Assessment Tool, and ran simulations for 2019–2021. By comparing simulations with and without dust nutrient inputs, we estimated the impact of dust‐deposited nutrients on individual watershed processes. Results revealed a significant contribution of dust‐deposited nutrients, particularly soluble reactive phosphorus (SRP), to several nutrient cycling and transport pathways. Notably, dust contributed up to 19.3% of the SRP load in annual streamflow (increasing monthly streamflow concentration by up to 10.9 μg ). Spatial analysis of model estimates demonstrated a relationship between topography, soil type, and the cycling and transport of dust nutrients. The largest dust nutrient contributions were found in catchment areas with lower slope and less hydric soils, where other natural mobilization processes may be limited. This comparative modeling approach stresses the importance of including dust nutrients in watershed models, especially in oligotrophic systems, and has potential to validate these findings elsewhere and identify how watershed characteristics may either mollify or accentuate the impacts of dust deposition on mountain freshwater systems.