This study aims to characterize geochemically the acid mine drainage (AMD) sources causing deterioration of the water quality of a river reach with extreme hydrologic variability and to identify the patterns of dissolved and particulate contaminants along the reach. The hydrochemistry of the river reach is exposed to dramatic seasonal and spatial changes. The levels of sulfate and metals increase progressively along the reach due to the input of the first AMD discharges. However, the confluence with the Agrio River, which collects extremely acidic and metal-rich AMD from Riotinto mines, causes the total depletion of alkalinity and a dramatic decrease of pH values (down to 3.3), which strongly enhances the solubility of metals. A pH-controlled pattern of metal transport prevails in the river. Above pH 6, particulate Al and Fe is the predominant form of transport in the river; below pH 5, Al is chiefly transported in dissolved form, while the water velocity may control sedimentation of Fe precipitates. Particulate Cu, Zn, and Mn exhibit a similar pattern although with some differences. Above pH 6, Cu is generally transported by the particulate phase, while Zn and to a greater extent Mn, are mostly carried by the dissolved phase. Cobalt and Ni are mostly transported in dissolved form, even at circumneutral pH values, showing a more conservative behavior. Geochemical modeling results and analysis of high-energy X-ray diffraction patterns point to schwertmannite and ferrihydrite as the mineral phases responsible for the solubility control of Fe. Schwertmannite may precipitate close to mixing zones, where lower pH values and higher sulfate concentrations are found, while ferrihydrite probably precipitates farther from these zones, at higher pH values and lower sulfate concentrations. Metal and sulfate loadings are strongly linked to rainfall events. The highest dissolved loads were observed during floods in May 2016, when up to 48 t day−1 of Al, 16 t day−1of Fe, 8.4 t day−1of Zn, and so on, were transported by the river, values noticeably higher than those observed in other mining areas.