There are several industrial processes in which heavy metals are used, including but not limited to chrome plating and tanning. Amongst the most toxic heavy metals to human health are arsenic, cadmium, chromium, lead, copper, nickel, and mercury. The aforementioned toxic metals possess the ability to cause contamination upon their release into the environment. Humans and aquatic and terrestrial animals are at risk from heavy metals in water and soil. Heavy metal toxicity has the potential to result in several health complications, such as renal and hepatic impairment, dermatological afflictions, cognitive lethargy, and potentially oncogenic manifestations. The removal of heavy metals from wastewater and soil can be accomplished using a variety of conventional methods, such as membrane filtration, reverse osmosis, chemical reduction, and adsorption. These methods have several disadvantages, such as generating an abundance of secondary pollutants, and entail significantly higher costs in comparison to biological methods. Conversely, eco-friendly techniques based on microbes have numerous advantages. This review provides a comprehensive overview of biological processes that remove heavy metal ions, both metabolically dependent and metabolically independent. Additionally, we also focused on the source and toxicity of these heavy metals. This study is expected to be particularly beneficial for the development of biological heavy metal treatment systems for soil and water.