Contaminant metals derived from acid mine drainage (AMD) are transported through stream networks in aqueous, colloidal, and/or particulate phases; however, hydrogeochemical processes that regulate export of these phases from headwater catchments are not fully resolved. We investigated metal speciation and transport along redox and pH gradients and as a function of discharge in an AMD-impaired stream. Contaminated groundwater upwelling into the stream mixed first with oxygenated surface water and then with alkaline effluent from a treatment system. Contaminant Fe was effectively removed from the stream as Fe2+ oxidation generated Fe(III)-bearing colloids that rapidly aggregated and accumulated in streambed sediments. Iron precipitated first as Fe(III) (oxyhydr)oxides but then as oxyhydroxysulfates as Fe hydrolysis lowered stream pH. Smaller amounts of Fe2+ were incorporated into framboidal pyrite in oxygen-poor sediments. Conversely, AMD-derived Mn2+ and Al3+ were only minimally removed from the stream during seasonal mixing with treated effluent. Although natural attenuation limited Fe export from the watershed, Fe stored in stream sediments has the potential to be remobilized due to oxidative dissolution of Fe-sulfides and/or physical scouring of the streambed. This work demonstrates how colloid formation and mobility respond to geochemical gradients, with implications for how sediment–water interactions influence metal transport through streams.