Reclamation and re-vegetation of excavated sediments can represent major environmental challenges. This study was conducted to compare CaCO3 and Ca(OH)2 as amendments for pH control in the environmental management of a circum-neutral Mn-, Zn-, and Cu-contaminated sediment in which re-vegetation was unsuccessful. The specific objectives were to evaluate the relative impacts of these treatments on localization and solubility of Mn, Zn, and Cu, as well as potential bioavailability. Sediment samples were collected from Milltown Reservoir, Montana, USA and analyzed before, during, and after oxidative incubation. The mineralogical analyses included composition (X-ray diffraction), control of metals solubility (by chemical equilibrium), and localization of Cu, Mn, and Zn (SEM-EDS; selective extraction procedures). The concentrations of Mn, Zn, and Cu in solution were determined by ICP-OES and atomic absorption spectroscopy. The sediment was composed principally of quartz, feldspars, phyllosilicates, gypsum, trace sulfide minerals, and 15.5 g kg−1 organic carbon. Upon CaCO3 treatment, pH increased from 7.0 to 7.5 from day 1 to day 48, compared to the Ca(OH)2 treatment which resulted in an initial pH > 11, subsequent decrease to pH 8–8.5 within the same period, and the concomitant precipitation of secondary carbonate and silicate phases. Due to the different chemistries of the CaCO3 and Ca(OH)2 reaction systems, Ca(OH)2 was significantly (p < 0.05) more effective than CaCO3 in reducing soluble, ion-exchangeable, and adsorbed Mn and Zn concentrations. The solubilities of Mn and Zn were controlled by rhodochrosite and willemite, respectively. Slight increases in Cu solubility with the Ca(OH)2 treatment were attributable to partially non-reversible increased dissolved organic matter and Cu-organic complex concentrations. The results of the study reflected the different chemistries of the CaCO3 and Ca(OH)2 systems. With the Cu-, Mn-, and Zn-polluted Milltown sediment, the Ca(OH)2 treatment offered significant advantages compared to the CaCO3 treatment in metals immobilization; however, each reclamation site can have unique sediment properties and should be considered independently. The solubilities of Cu-, Mn-, and Zn- minerals controlling equilibria are highly pH dependent; hence, pH control may be an essential component of effective site management for circum-neutral sediments.