Microbial bioremediation and biodegradation in environmental monitoring offers an environmentally friendly approach for the monitoring and effective removal of contaminants. Various aspects of microbial-mediated bioremediation take advantage of the microorganisms’ ability to transform noxious compounds into utilizable intermediates and value-added products. Different microbial metabolites such as enzymes, biosurfactants, emulsifiers, organic acids, and solvents play significant roles in the decontamination of radioactive and heavy metals, chemical pesticides, and organic contaminants such as dyes and hydrocarbons in environmentally safe manners. Recent advancements in biochemical engineering, OMICS and genetic modification, and synthetic-biology pave ways for identifying indicator microbial strains, mechanisms of remediation, and the development of tailor-made microbe-metabolites for future applications. Microbial biotechnology in environmental monitoring and bioremediation thus represent a new way to rehabilitate and reconstruct “damaged” ecosystems. This work summarizes the latest research in the field of environmental bioremediation and offers fascinating insights on the behaviours of these unique microorganisms. It also presents exciting, new perspectives for the application of microbes in environmental protection. It is suitable for students, scholars, researchers and organizations involved in environmental protection.