Abstract The Pinal creek drainage basin in Arizona is a good example of the principal non-coal source of mining-related acid drainage in the U.S.A., namely copper mining. Infiltration of drainage waters from mining and ore refining has created an acid groundwater plume that has reacted with calcite during passage through the alluvium, thereby becoming less acid. Where O 2 is present and the water is partially neutralized, iron oxides have precipitated and, farther downstream where the pH of the stream water is near neutral, high-Mn crusts have developed. Trace metal composition of several phases in the Pinal Creek drainage basin illustrates the changes caused by mining activities and the significant control Mn-crusts and iron oxide deposits exert on the distribution and concentration of trace metals. The phases and locales considered are the dissolved phase of Webster Lake, a former acid waste disposal pond; selected sections of cores drilled in the alluvium within the intermittent reach of Pinal Creek; and the dissolved phase, suspended sediments, and streambed deposits at specified locales along the perennial reach of Pinal creek. In the perennial reach of Pinal Creek, manganese oxides precipitate from the streamflow as non-cemented particulates and coatings of streambed material and as cemented black crusts. Chemical and X-ray diffraction analyses indicate that the non-cemented manganese oxides precipitate in the reaction sequence observed in previous laboratory experiments using simpler solution composition, Mn 3O 4 to MnOOH to an oxide of higher oxidation number usually <4.0, i.e. Na-birnessite, and that the black cemented crusts contain (Ca,Mn,Mg)CO 3 and a 7-Åphyllomanganate mixture of rancieite ((Ca,Mn)Mn 4O 9 · (3H 2O)) and takanelite ((Mn,Ca)Mn 4O 9 · (3H 2O)). In the laboratory, aerating and increasing the pH of Pinal Creek water to 9.00 precipitated (Ca,Mn,Mg)CO 3 from an anoxic groundwater that contained CO 2 HCO 3, and precipitated Mn 3O 4 and subsequently MnOOH from an oxic surface water from which most of the dissolved CO 2 had been removed. It is suggested that the black cemented crusts form by precipitation of Fe on the Mn-enriched carbonates, creating a site for the Mn Fe oxidation cycle and thus encouraging the conversion of the carbonates to 7-Åphysllomanganates. The non-magnetic <63-μm size-fractions of the black cemented crusts consisted mostly of the manganese-calcium oxides but also contained about 20% (Ca,Mn,Mg)CO 3, 5% Fe (calculated as FeOOH), 2–4% exchangeable cations, and trace amounts of several silicates.