Industrialization and urbanization are the major contributors of heavy metal pollution in the wastewater, which should be controlled through novel, efficient, and environmentally friendly methods. Biologically based heavy metal treatment methods are attractive and advantageous compared to physical and chemical methods. Here, we have reviewed emerging microbial technological methods such as bioremediation (use of bacteria in the form of bioaugmentation, bioventing, and biofilters with removal potential of heavy metals ranged from 60% to 95% within 48–96 h), mycoremediation (use of fungi with removal potential of heavy metals ranged from 60% to 95% within 2–8 weeks), phycoremediation (use of algae with removal potential of heavy metals ranged from 50% to 95% within 24–120 h), biogenic nanoparticles (use of biological originated nanoparticles in the form of carbon nanotubes, graphene nanotubes, silica-based nanomaterials, zero-valent metal nanomaterials, and metal oxide nanomaterials) and bioorganic amendments (use of compost, biochar, and biofertilizers), which are being used and reported for the treatment of wastewater contaminated with heavy metals. These techniques or amendments removed heavy metals from wastewater through biosorption, bioaccumulation, bioprecipitation, biotransformation, and detoxification mechanisms. Based on the data reviewed here, it can be concluded that bioremediation and phycoremediation are the most efficient and time-saving techniques that could be employed to treat heavy metals from wastewater.