Rapid development and urbanisation have increased land, water, and soil pollution levels. Many new technologies have been established to aid in the recycling and treatment of such harmful pollutants, but such modern procedures have drawbacks such as high prices and the generation of resistant toxic chemicals. With such negative environmental impacts, a safe and convenient biological approach in the form of microbial strains enters the picture as these microorganisms are known to exhibit a variety of biosynthetic activities. This characteristic of microorganisms aids in the resolution of several problems, including the treatment of oil spills that have damaged the environment, industrial effluent management, and waste management. Microbes contribute to ecological equilibrium by participating in biogeochemical cycles. Microbes play a significant role in nutrient cycling, which benefits soil and plant health. Furthermore, a variety of microorganisms break down harmful substances that have entered the soil as a result of the widespread use of chemical pesticides and fertilisers. DGGE and other molecular techniques have been widely used in waste treatment. This chapter focuses on the different ways that microbes are used in molecular-based environmental maintenance techniques, heavy metal detoxification, bioremediation, and cleanup of contaminated areas.