A series of column experiments was conducted using manganese oxide coated sediments collected from the hyporheic zone in Pinal Creek (AZ), a metal-contaminated stream, to study the uptake and retention of Mn, Ni, and Co. Experimental variables included the absence (abiotic) and presence (biotic) of active Mn-oxidizing bacteria, the absence and presence of dissolved Mn, and sediment manganese oxide content. Uptake of Mn under biotic conditions was between 8 and 39% higher than under abiotic conditions. Continuous uptake of Mn due to biotic oxidation was evident from extraction of column sediments. Manganese uptake is hypothesized to initially occur as adsorption, which led to subsequent surface and/or microbial oxidation. Complete breakthrough of Ni within 100 pore volumes indicated no process of continuous uptake and was modeled as an equilibrium adsorption process. Nickel uptake in the presence of dissolved Mn was 67-100% reversible. Sediment extractions suggest that Ni uptake occurred through weak and strong adsorption. Continuous uptake of cobalt increased with sediment manganese oxide content, and Co uptake was up to 75% greater under biotic than abiotic conditions. Cobalt uptake was controlled by both existing and newly formed manganese oxides. Only a small amount of Co uptake was reversible (10-25%). XANES spectral analysis indicated that most Co(II) was oxidized to Co(III) and probably incorporated structurally into manganese oxides. Although manganese oxides were the primary phase controlling uptake and retention of Mn, Ni, and Co, the mechanisms varied among the metals.