Biofilter is one of the most important separation processes that can be employed to remove organic pollutants from air, water, and wastewater. Even though, it has been used over a century, it is still difficult to explain theoretically all the biological processes occurring in a biofilter. In this paper, the fundamental of biological processes involved in the biofilter is critically reviewed together with the mathematical modeling approach. The important operating and design parameters are discussed in detail with the typical values used for different applications. The most important parameter which governs this process is the biomass attached to the medium. The relative merits of different methods adopted in the measurement of the biomass are discussed. The laboratory-and full-scale applications of the biofilter in water and wastewater treatment are also presented. Their performances in terms of specific pollutant removal are highlighted.