Although recent construction of tailings dams has dramatically decreased solids discharge rates, pyrite-dominated polymetallic sulfide mine tailings persist as the primary in-stream substrate of the upper Rio Pilcomayo, a crucial water resource in the arid Southeastern Bolivian highlands. Rio Tarapaya is a primary tributary of the upper Rio Pilcomayo that drains Potosí, Bolivia, where intensive hard rock mining and ore processing has occurred for five centuries. In conjunction with standard water quality testing, field leach tests were performed on saturated sediment within the active channel as well as unsaturated sediment deposited on the banks of the Rio Tarapaya during highflow events. Results indicate that weathering of in-stream tailings is contributing to deleterious concentrations of various ecotoxic metals. Of special concern is the mobilization of metals and acidity with increases in water level, such as occurs at the onset of the rainy season. The highly seasonal, arid climate provides for long periods of mineral oxidation followed by large precipitation events which mobilize weathered oxidation products. The reactivity of the millions of tonnes of in-stream tailings in Rio Tarapaya suggests that the upper Rio Pilcomayo will remain severely degraded for the foreseeable future and remediation will continue to be a daunting task.