I am sure most of you are familiar with cycling an aquarium. If not, check out this video.

Cycling your aquarium is so crucial because it allows time for beneficial bacteria to grow in your aquarium and establish your biological filtration. In this video, we are going to discuss biological filtration and provide you with the necessary information to ensure you are providing the right kind of environment for beneficial bacteria to thrive in your tank.

The term biological filtration refers to the various beneficial bacteria that grow on just about every surface submerged in your aquarium. This bacteria breaks down and processes waste into less harmful byproducts essentially filtering your aquarium water.

So how does one go about providing biological filtration? Well, it is quite easy because nature does the work for you. Naturally, beneficial bacteria will grow on any surface submerged in your tank; biological filter media, rocks, substrate, decorations, pumps, tank walls, etc.

For fish-only systems and freshwater aquariums, the use of bio-balls, a wet/dry filter, or other biological filter media provides extra surface area for bacteria to grow. Boosting the bacteria population means waste is processed more effectively; in turn creating a healthier environment for your fish.

When keeping a reef tank, the use of biological filter media is generally not recommended because they are so effective at trapping and processing waste. If the media is not cleaned frequently, it is very difficult to keep nitrate levels at a minimum and elevated nitrate levels in a reef tank can lead to some serious problems for your corals and invertebrates as well as contribute to nuisance algae outbreaks.

Thankfully, with the use of live rock for biological filtration in a reef tank, we can control waste and help avoid elevated nitrate levels. Live rock will host a variety of different bacteria both on the surface as well as deep within the pores of the rock. Aerobic bacteria growing on the outer surfaces that are exposed to fresh oxygenated water will break down nitrite and ammonia. The denitrifying bacteria living deep within the rock called anaerobic bacteria will break down nitrate. This is why live rock is such an effective biological filter media; it will help to process and filter out all three byproducts of the nitrogen cycle; ammonia, nitrite, and nitrate.

But what if you don’t want to go with live rock and would prefer to use dry rock for your reef tank? Can you still get the same results? The short answer is yes, but it will simply take more time for the bacteria to colonize the rock. Using a bacterial supplement, such as the Brightwell Microbacter7, can help seed the rock to get the process moving along quicker. Regular addition of the bacterial supplement will help to maintain a healthy population and diversity of bacteria strains.

Your sand bed is also another crucial environment for bacteria to grow because of the amazing amount of surface area the sand provides for bacteria to grow. The use of a shallow sand bed will provide a great environment for aerobic bacteria to process nitrite and ammonia. If you choose to run a deep sand bed, more than 2-3” deep, you will effectively grow anaerobic bacteria as well to help control nitrate. The same case applies with using dry sand vs live sand, both have the capability to host bacteria but live sand comes with bacteria already colonized while dry sand will simply take a bit longer to establish in your tank.

Biological Filter Media
  1. MicroBacter Lattice XL - Biological Filtration Media
    Brightwell Aquatics
    MicroBacter Lattice XL - Biological Filtration Media

  2. Xport-BIO Freshwater Plate - Biological Filtration Media
    Brightwell Aquatics
    Xport-BIO Freshwater Plate - Biological Filtration Media


One key thing to remember about the bacteria that break down waste products in aquariums, the vast majority of them will adhere to surfaces somewhere in the tank, they will not be free-floating. Therefore, doing water changes should not affect the biological filtration in an established aquarium when performed properly.

The correct application of biological filtration in conjunction with a protein skimmer, refugium, bio-pellets, and/or other types of filters can help keep your tanks' water pristine and your fish, invertebrates, and corals happy and healthy.