The ability of heavy metals bioaccumulation to cause toxicity in biological systems—human, animals, microorganisms and plants—is an important issue for environmental health and safety. Recent biotechnological approaches for bioremediation include biomineralization (mineral synthesis by living organisms or biomaterials), biosorption (dead microbial and renewable agricultural biomass), phytostabilization (immobilization in plant roots), hyperaccumulation (exceptional metal concentration in plant shoots), dendroremediation (growing trees in polluted soils), biostimulation (stimulating living microbial population), rhizoremediation (plant and microbe), mycoremediation (stimulating living fungi/mycelial ultrafiltration), cyanoremediation (stimulating algal mass for remediation) and genoremediation (stimulating gene for remediation process). The adequate restoration of the environment requires cooperation, integration and assimilation of such biotechnological advances along with traditional and ethical wisdom to unravel the mystery of nature in the emerging field of bioremediation. This review highlights better understanding of the problems associated with the toxicity of heavy metals to the contaminated ecosystems and their viable, sustainable and eco-friendly bioremediation technologies, especially the mechanisms of phytoremediation of heavy metals along with some case studies in India and abroad. However, the challenges (biosafety assessment and genetic pollution) involved in adopting the new initiatives for cleaning-up the heavy metals-contaminated ecosystems from both ecological and greener point of view must not be ignored.