Metal concentrations were determined in benthic biota, fish livers, water, and fine-grained sediment through 215 km of an intermontane river system (Blackfoot River, Montana, USA) affected by headwater inputs of acid-mine effluent. Solute and particulate contaminants decreased rapidly downstream from headwater sources, but some extended through an extensive marsh system. Particulate contaminants penetrated through the marsh system, effectively resulting in food web contamination downstream of the marshes. Metals differed in their bioavailability within and below the marsh system. Cadmium was most consistently accumulated in the food web, and the general order of downstream mobilization of bioavailable metals appears to be Cd, Zn > Cu > As, Ni. Depauperate benthic communities and reduced fish populations occurred coincident with the sediment contamination.