We investigated the transport of dissolved arsenic (As) in groundwater, surface water, and the hyporheic zone of a stream-aquifer system influenced by an abandoned arsenopyrite mine. The weathering of unconsolidated aquifer materials, derived from mine waste piles, consists of As-bearing minerals including arsenopyrite, scorodite, and iron oxides, providing a continuous source of As to water. Arsenic loads from the stream, springs, and groundwater were quantified at the study reach on nine dates from January to August 2005, and a mass balance approach was used to determine hyporheic storage of As. Loading from groundwater was the dominant source of As to the stream, while loads from springs represented a substantial proportion of the As load during spring. Arsenic loads in surface and groundwater were significantly elevated during summer despite lower discharge; groundwater load was positively correlated to aquifer temperature. The hyporheic zone retained As in the upstream-most subreach, most likely through the adsorption of As onto hyporheic sediments. In downstream subreaches, hyporheic sediments, derived from mine-tailing piles of high As content, were sources of As to the stream. Spatial variation in sediment source and composition reflecting flood transport from upstream and mass wasting of mine tailings, along with temporal changes in hydrology, combine to dictate the role of the hyporheic zone in the transport and retention of As.