Because filtration and growth of biomass leads to an accumulation of matter in the filtering media, this type of fixed-film process is subject to bioclogging and flow channeling. Depending on the type of application and on the media used for microbial growth, bioclogging can be controlled using physical and/or chemical methods. Backwash steps can be implemented using air and/or water to disrupt the biomat and recover flow whenever possible. Chemicals such as oxidizing (peroxide, ozone) or biocide agents can also be used.
Biofiltration can require a large area for some treatment techniques (suspended growth and attached growth processes) as well as long hydraulic retention times (anaerobic lagoon and anaerobic baffled reactor).