Heavy metals are hazardous and bring about critical exposure risks to humans and animals, even at low concentrations. An assortment of approaches has been attempted to remove the water contaminants and keep up with water quality, for that microbial bioremediation is a promising way to mitigate these pollutants from the contaminated water. The flexibility of microorganisms to eliminate a toxic pollutant creates bioremediation an innovation that can be applied in various water and soil conditions. This review insight into the sources, occurrence of toxic heavy metals, and their hazardous human exposure risk. In this review, significant attention to microbial bioremediation for pollutant mitigation from various ecological lattices has been addressed. Mechanism of microbial bioremediation in the aspect of factors affecting, the role of microbes and interaction between the microbes and pollutants are the focal topics of this review. In addition, emerging strategies and technologies developed in the field of genetically engineered micro-organism and micro-organism-aided nanotechnology has shown up as powerful bioremediation tool with critical possibilities to eliminate water pollutants.