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Environmental pollution, especially water pollution, is increasing in the ecosystem, causing a scarcity of clean water for life. Water pollution from heavy metals occurs due to anthropogenic activities during the industrial use of heavy metals. Although some metals are essential for environmental survival, most heavy metals (Pb, Ag, Hg, Cd, As, Ni, Cu, Cr, Co, and Zn) are highly toxic and enter the food chain, disrupting the chain and negatively impacting human health. Exposure to heavy metals can damage kidneys, lungs, liver, cancer, and even death in acute cases. Recently, genetically modified microorganisms (GMMs) produced by recombinant technologies have been used as an alternative for the bioremediation of toxic metals. The GMMs produce many enzymes and metabolites to resist and convert toxic metals into non-toxic forms. Recent advances in genetics have allowed scientists to transfer desired genes into fast-growing microorganisms and increase the efficiency of genes to remove heavy metals. The review focuses on the recent advances in developing GMMs and their applications in effectively removing heavy metals such as mercury, arsenic, cadmium, chromium, lead, nickel, copper, zinc, silver, and cobalt. This review also highlights this technique's potential challenges and risks and the prospects of using GMMs.