Currently, industry in all its forms is vital for the human population because it provides the services and goods necessary to live. However, this process also pollutes soils and rivers. This research provides an environmentally friendly solution for the generation of electrical energy and the bioremediation of heavy metals such as arsenic, iron, and copper present in river waters used to irrigate farmers’ crops. This research used single-chamber microbial fuel cells with activated carbon and zinc electrodes as anodes and cathodes, respectively, and farmers’ irrigation water contaminated with mining waste as substrate. Pseudomonas stutzeri was used as a biocatalyst due to its ability to proliferate at temperatures between 4 and 44 °C—at which the waters that feed irrigated rivers pass on their way to the sea—managing to generate peaks of electric current and voltage of 4.35 mA and 0.91 V on the sixth day, which operated with an electrical conductivity of 222 mS/cm and a pH of 6.74. Likewise, the parameters of nitrogen, total organic carbon, carbon lost on the ignition, dissolved organic carbon, and chemical oxygen demand were reduced by 51.19%, 79.92%, 64.95%, 79.89%, 79.93%, and 86.46%. At the same time, iron, copper, and arsenic values decreased by 84.625, 14.533, and 90.831%, respectively. The internal resistance values shown were 26.355 ± 4.528 Ω with a power density of 422.054 mW/cm2 with a current density of 5.766 A/cm2. This research gives society, governments, and private companies an economical and easily scalable prototype capable of simultaneously generating electrical energy and removing heavy metals.