We determined the role of the hyporheic zone (the subsurface zone where stream water and shallow groundwater mix) in enhancing microbially mediated oxidation of dissolved manganese (to form manganese precipitates) in a drainage basin contaminated by copper mining. The fate of manganese is of overall importance to water quality in Pinal Creek Basin, Arizona, because manganese reactions affect the transport of trace metals. The basin-scale role of the hyporheic zone is difficult to quantify because stream-tracer studies do not always reliably characterize the cumulative effects of the hyporheic zone. This study determined cumulative effects of hyporheic reactions in Pinal Creek basin by characterizing manganese uptake at several spatial scales (stream-reach scale, hyporheic-flow-path scale, and sediment-grain scale). At the stream-reach scale a one-dimensional stream-transport model (including storage zones to represent hyporheic flow paths) was used to determine a reach-averaged time constant for manganese uptake in hyporheic zones, 1/λ_s, of 1.3 hours, which was somewhat faster but still similar to manganese uptake time constants that were measured directly in centimeter-scale hyporheic flow paths (1/λ_h= 2.6 hours), and in laboratory batch experiments using streambed sediment (1/λ = 2.7 hours). The modeled depths of subsurface storage zones (d_s = 4–17 cm) and modeled residence times of water in storage zones (t_s = 3–12 min) were both consistent with direct measurements in hyporheic flow paths (d_h = 0–15 cm, t_h = 1–25 min). There was also good agreement between reach-scale modeling and direct measurements of the percentage removal of dissolved manganese in hyporheic flow paths (f_s = 8.9%, andf_h = 9.3%rpar;. Manganese uptake experiments in the laboratory using sediment from Pinal Creek demonstrated (through comparison of poisoned and unpoisoned treatments) that the manganese removal process was enhanced by microbially mediated oxidation. The cumulative effect of hyporheic exchange in Pinal Creek basin was to remove approximately 20% of the dissolved manganese flowing out of the drainage basin. Our results illustrate that the cumulative significance of reactive uptake in the hyporheic zone depends on the balance between chemical reaction rates, hyporheic porewater residence time, and turnover of streamflow through hyporheic flow paths. The similarity between the hyporheic reaction timescale (1/λ_s ≈ 1.3 hours), and the hyporheic porewater residence timescale (t_s ≈ 8 min) ensured that there was adequate time for the reaction to progress. Furthermore, it was the similarity between the turnover length for stream water flow through hyporheic flow paths (L_s = stream velocity/storage-zone exchange coefficient ≈ 1.3 km) and the length of Pinal Creek (L ≈ 7 km), which ensured that all stream water passed through hyporheic flow paths several times. As a means to generalize our findings to other sites where similar types of hydrologic and chemical information are available, we suggest a cumulative significance index for hyporheic reactions, R_s = λ_st_sL/L_s (dimensionless); higher values indicate a greater potential for hyporheic reactions to influence geochemical mass balance. Our experience in Pinal Creek basin suggests that values of R_s > 0.2 characterize systems where hyporheic reactions are likely to influence geochemical mass balance at the drainage-basin scale.