The Snake River watershed is typical of many river systems in the Rocky Mountains in that it contains sources of acidity and trace metals from both natural weathering of disseminated pyrite and from acid rock weathering associated with past mining operations. The seasonal variation in hydrology is dominated by melting of the snowpack in spring. We have monitored seasonal variations in the chemistry of the Snake River system beginning in 1980 with a few gaps in the record and with sampling frequency ranging from weekly during some snowmelt periods to monthly. The results show that the spring flood controls the stream water chemistry by several processes. Firstly, the concentrations of sulfate and metals from natural pyrite weathering decrease during spring snowmelt due to dilution. In contrast, the concentrations of some metals, especially zinc, increase probably due to direct runoff from the surface of tailings piles and from flushing of upper soils horizons in mined areas. The concentrations of metals in the streamwater is also controlled by instream reactions, predominantly precipitation of iron and aluminum oxides, coprecipitation/sorption of dissolved humic substances, sorption of other trace metals by oxides, and iron photochemistry. The chemical interactions are greatly influenced by the hydrologic regime. In years of high snowpack more zinc is mobilized from the catchment than in years of low snowpack.