Heavy metal pollution in water has become a global environmental problem, threatening aquatic ecosystems and human health. Physical and chemical methods can effectively remove heavy metal pollutants, while their applications are limited due to the high costs, complex operation, and susceptibility to secondary pollution. Bioremediation is the most promising method for eliminating toxic pollutants. Microorganisms including bacteria, fungi, and algae can convert toxic heavy metals into less toxic forms, which has become an effective and environmentally friendly solution for the remediation of heavy metal pollution in water environments. This paper expounds the toxicity and mechanism of heavy metal pollution, microbial remediation mechanisms, and primary microbial remediation strategies, providing a reference for the removal or reduction of metal pollutants in water environments as well as the development of related technologies.