Biological filtration utilizes living organisms to remove substances from aquatic systems as a natural result of their respiration and metabolic processes. This mode of filtration is at work in any aquarium system housing live organisms. Though microbes (e. g. bacteria) are arguably responsible for the majority of nutrient-remineralization that takes place, oceanographic studies have shown that up to 90% of the dissolved organic carbon present in seawater may be assimilated by planktonic bacteria (bacterioplankton).

This nutrient assimilation simultaneously removes nitrogen (as ammonia, nitrite, and nitrate) and phosphorus (as phosphate) from the water, making bacterioplankton a very effective sink of dissolved organic material that would otherwise fuel the growth of organisms such as cyanobacteria and filamentous algae in aquaria. Bacterioplankton are also an important food source for organisms that are able to capture them from the water column.

In a sense, utilizing these microbes to control dissolved organic material and then gradually removing the microbes themselves on a continuous basis through protein skimming and the feeding activities of corals, clams, tube worms, tunicates, sponges, and their respective allies, becomes an effective means of nutrient-harvest. Simultaneously, it promotes the health of these suspension-feeding organisms through constant feeding (encouraging polyp-expansion in many types of corals), and promotes water quality.

The entire process requires that adequate carbon be present in a usable form. In aquaria with a tendency towards elevated phosphate and nitrate concentrations, an appropriate source of carbon may quickly become depleted. Reef BioFuel provides a source of bioavailable carbon to ensure that nutrient remineralization is efficient and effective.