Generation of wastewater is just unavoidable but its discharge into the environment is of great concern. Wastewater mainly comprised of any unwanted waste that could pollute our water system including sewage sludge, wastewater from domestic, industrial, dairy, fish canning and oil and gas industry. Since the early 1990s, microbial treatment processes have gained increasing attention due to its facility and high efficiency compared to conventional techniques. This paper focuses on the essential mechanisms involved in different microbial treatment techniques and special attention on the most recent challenges and developments will be highlighted in this review.