Mining influenced water (MIW) derived from mining and metallurgical operations may require treatment prior to beneficial use or release of the water. Constituents in MIW that may require removal include: metals, metalloids, radionuclides, acidity, sulfate and nitrogen species. Microorganisms are capable of facilitating the removal of the above constituents through biogenic reagent production for precipitation or neutralization; oxidation or reduction of redox active metals, metalloids and radionuclides; and sulfur and nitrogen transformations. Harnessing the diverse capabilities of the microbial world requires us to create the appropriate environment or sequence of environments to promote the desired transformations. Removal of many constituents in MIW requires a synergy between biotic and abiotic reactions. Thus, in addition to the appropriate environment for the targeted microbial transformation we must be cognizant of the requirements of the abiotic reactions. This paper summarizes and systematizes the current understanding of the biotic and abiotic reactions needed to remove the diverse target constituents from MIW. The biotic reactions require sufficient substrate and nutrients and a microbial population that can mediate the desired transformation. The abiotic reactions require appropriate redox and chemical conditions to promote formation of the desired end products. The conditions required for each of the target constituents (metals, metalloids, radionuclides, acidity, sulfate and nitrogen species) are varied. The goal of this paper is to examine each group of target constituents and to discuss the required transformations and environmental conditions for successful bioremediation of MIW.