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Fish and invertebrates produce wastes, in the form of feces and ammonia, which are harmful if they build up (consider if you had to live in your toilet!); an aquarium's biological filter consists of organisms which break down these wastes into less-harmful and, ideally, ultimately harmless byproducts.

Detrivorous invertebrates such as snails and some crustaceans are perhaps the first step of the biological filter, as they will eat and derive nutrition from fresh or decomposed fish feces, unnoticed carrion (corpses), and rotting plant matter, in turn producing their own wastes. They are non-essential, as ultimately this macroscopic detritus will be broken down by bacteria, but they do aid the process considerably if present.

The macroscopic detritus is ultimately metabolized to simple molecules, most notably but not limited to CO2 and ammonia or nitrate. CO2 and ammonia are also produced directly by fish and invertebrates through respiration and excretion. The former evaporates into the air or is taken up by plants and algae; the latter must be broken down further. At low pH, the ammonia is protonated and is present in the form of ammonium ions; at high pH it is present as molecular ammonia, which is quite toxic to fish and invertebrates.

Both forms may be removed by plant and algae metabolism; this is ideal, but it is very rare for aquarium plant and algae growth to be nitrogen-limited. Nitrosomonas and similar bacteria oxidize the rest, yielding nitrite ions. Nitrite is also rather toxic, binding tightly, not unlike CO2 to oxygen-carrying metalloproteins such as hemoglobin and hemocyanin. Nitrobacter further oxidize the nitrite to less toxic nitrate. Nitrate lingers to be metabolized by plants which were perhaps beaten by the Nitrosomonas to metabolizing the ammonia, but, again, as aquarium plant growth is rarely nitrogen limited, it usually builds up. In concentrations greater than about 30 ppm, it is a stressor of fish; invertebrates and some sensitive fish species tolerate even less, hence, regardless of what is being kept in the aquarium, regular water changes are necessary.

If an anoxic environment is provided somewhere in the aquarium system, a further step called denitrification takes place, in which bacteria selectively use nitrate and nitrite as electron acceptors in place of oxygen. This condition is achieved in several ways, namely the old-fashioned "plenum", consisting of a raised plastic plate under a section of the sand or gravel, the proprietary

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