The first treatise on mining and extractive metallurgy, published by Georgius Agricola in 1556, was also the first to highlight the destructive environmental side effects of mining and metals extraction, namely dead fish and poisoned water. These effects, unfortunately, are still with us. Since 1556, mining methods, knowledge of metal extraction, and chemical and microbial processes leading to the environmental deterioration have grown tremendously. Man’s insatiable appetite for metals and energy has resulted in mines vastly larger than those envisioned in 1556, compounding the deterioration. The annual amount of mined ore and waste rock is estimated to be 20 billion tons, covering 1,000 km2. The industry also annually consumes 80 km3 of freshwater, which becomes contaminated. Since metals are essential in modern society, cost-effective, sustainable remediation measures need to be developed. Engineered covers and dams enclose wastes and slow the weathering process, but, with time, become permeable. Neutralization of acid mine drainage produces metal-laden sludges that, in time, release the metals again. These measures are stopgaps at best, and are not sustainable. Focus should be on inhibiting or reducing the weathering rate, recycling, and curtailing water usage. The extraction of only the principal economic mineral or metal generally drives the economics, with scant attention being paid to other potential commodities contained in the deposit. Technology exists for recovering more valuable products and enhancing the project economics, resulting in a reduction of wastes and water consumption of up to 80% compared to “conventional processing.” Implementation of such improvements requires a drastic change, a paradigm shift, in the way that the industry approaches metals extraction. Combining new extraction approaches, more efficient water usage, and ecological engineering methods to deal with wastes will increase the sustainability of the industry and reduce the pressure on water and land resources. From an ecological perspective, waste rock and tailings need to be thought of as primitive ecosystems. These habitats are populated by heat-, acid- and saline-loving microbes (extremophiles). Ecological engineering utilizes geomicrobiological, physical, and chemical processes to change the mineral surface to encourage biofilm growth (the microbial growth form) within wastes by enhancing the growth of oxygen-consuming microbes. This reduces oxygen available for oxidation, leading to improved drainage quality. At the water–sediment interface, microbes assist in the neutralization of acid water (Acid Reduction Using Microbiology). To remove metals from the waste water column, indigenous biota are promoted (Biological Polishing) with inorganic particulate matter as flocculation agents. This ecological approach generates organic matter, which upon death settles with the adsorbed metals to the sediment. Once the metals reach the deeper, reducing zones of the sediments, microbial biomineralization processes convert the metals to relatively stable secondary minerals, forming biogenic ores for future generations. The mining industry has developed and thrived in an age when resources, space, and water appeared limitless. With the widely accepted rise of the Anthropocene global land and water shortages, the mining industry must become more sustainable. Not only is a paradigm shift in thinking needed, but also the will to implement such a shift is required for the future of the industry.