We investigated the hydrologic, geochemical, and biogeochemical controls on stream chemical composition on the Green Lakes Valley and Andrews Creek watersheds using the alpine hydrochemical model (AHM). Both sites had comparable data sets from 1994 and 1996, including high‐resolution spatial data and high‐frequency time series of hydrology, geochemistry, and meteorology. The model of each watershed consisted of three terrestrial subunits (soil, talus, and rock), with the routing between the subunits determined by spatial land cover data. Using 1994 data for model calibration and 1996 data for evaluation, AHM captured the dominant processes and successfully simulated daily stream chemical composition on both watersheds. These results confirm our procedure of using spatial and site‐specific field and laboratory data to generate an initial catchment model and then calibrating the model to calculate effective parameters for unmeasured processes. A net source of nitrogen was identified in the Andrews Creek watershed during the spring snowmelt period, whereas nitrogen was immobilized in the Green Lakes Valley. This difference was most likely due to the larger and more dominant area of talus in the Andrews Creek watershed. Our results also indicate that routing of snowmelt through either soil or talus material is sufficient for retention of H⁺ and release of base cations but that N retention is more important on areas mapped as soil. Owing to the larger ionic pulse and larger fraction of surface runoff the Green Lakes Valley was more sensitive to a doubling of wet deposition chemistry than the Andrews Creek watershed.