The constant increase in global population, coupled with existing water pollution has put a strain on water resources globally. In some parts of the world, millions of people do not have access to clean and safe drinking water. Conventional water purification processes have their limitations and most of those processes cannot be employed for the removal of new and emerging water pollutants that have arisen in recent years from novel industrial processes and technologies. Most of those traditional processes are also not environmentally sustainable and contribute to environmental pollution in one way or another. This has led researchers to explore more efficient and environmentally sustainable methods of producing clean water. Various organic methods, both conventional and contemporary have been discussed and tested by scientists for applications in water purification as they pose little to no risk to the natural environment. Among these, the concept of utilizing microorganisms and their various metabolic capabilities for the breakdown of water pollutants is significant. Microorganisms through their metabolic activities can breakdown pollutants via bioaugmentation and biodegradation, or produce bioflocculants that bind suspended pollutant particles, making their removal easier. These organisms have also been applied in microbial fuel cells and microbial electro-deionization, systems that generate electricity while purifying water. These methods of using microbes in water treatment could be fairly easy to scale up and almost seamlessly integrated into existing water treatment processes. In comparison to conventional chemical treatments, they are more cost effective, environmentally sustainable and produce less secondary pollution. This technology is very promising and could have limitless applications with proper development.