Common Problems with Aquarium Bio-Filtration and How to Avoid Them

June 5, 2020 Phil Overton

Whether you already have an aquarium at home or are setting up a new one, you’ve probably compared and considered the different types of filtration media that might be best for your tank. As you research which filtration methods to use, one of the things you should keep in mind is that if you don’t use the proper setup, product, or maintenance measures for your tank, you will likely run into a few issues down the line with your filters, which, as a result, could affect the health of your tank.

In this article, we’re going to explain some issues that might arise when using biological-based filtration units by exploring a few common problems with aquarium bio-filtration and how to avoid them, so that when you do decide which type of filtration is best, you can be sure you’re setting up and maintaining everything correctly, keeping your fish healthy and your tank looking great.


The aquarium’s bio-filtration media doesn’t have enough time to “cycle”

Every new aquarium needs time to “cycle” or form enough beneficial bacteria that will keep the tank’s ammonia and nitrite levels in check. If you add your fish before the denitrifying bacteria have time to grow, ammonia and nitrite levels can accumulate to unsafe levels and harm or kill your fish, so allowing the bacteria enough time to proliferate in your bio-filtration media is key.

The time cycling loading rates how large the aquarium is, what plants or inanimate objects are present, and what measures you take, if any, to speed up the process. Some people use store-bought bacteria to get the process started or use a well-established piece of bio-filtration media from an older tank. You can also add fish food to the water, which will break down and decay, going through your filtration setup and feeding those beneficial organisms. But on average, this process could take one to two months. This is when you’ll need a reliable water testing kit, and over time, you’ll first see an increase in ammonia, which will peak and drop. Then you’ll notice the nitrates go up and come down. Once both of these peak and decrease, your tank should be ready for fish.


The aquarium’s bio-filtration media is clogging  

Some bio-filtration media, like sponges, work by drawing the contaminated water around it in and up through the media, catching plant and fish-waste debris in its fibers while allowing the filtered water to pass through, up, and out along with oxygen. These filters are great for removing larger particles from your tank and fostering a healthy rate of beneficial bacteria growth (the bacteria will grow along and inside all the little fibers and surfaces), but because they are constantly catching this debris, the debris accumulates and the media will need to be removed and cleaned often.

When you are using bio-filtration media, part of the magic happens when the bacteria are able to grow in number and stabilize. These filtration units provide a larger amount of surface area for denitrifying bacteria to proliferate, increasing your tank’s ability to maintain its control of ammonia and nitrites, providing a healthier ecosystem for your fish. When your bio-filtration media clogs often and you have to continually remove and clean it, you are disturbing those beneficial bacteria and forcing your media to constantly start from scratch, which could result in ammonia spikes that could harm your fish. This is also the reason to not use tap water, especially if your tap water has chlorine in it. This will kill the bacteria too, and similarly you’ll have to start all over again.

Try to find bio-filtration media that is designed to remain in place so that once your beneficial bacteria community is established it can continue to work—or, at the very least, consider setting up your tank with a combination of both mechanical filtration and bio-filtration so that your aquarium has the ability to both remove larger plant material and fish waste while providing a steady, reliable habitat for your bacteria.


The aquarium’s bio-filtration media doesn’t provide enough surface area

Some bio-filtration media provide less surface area than others (for example, plastic moving-bed or bio-ball filter media versus ceramic bio-filter media). When the media has a lot of room between its surfaces and doesn’t provide space for anaerobic bacteria (or bacteria that don’t require oxygen) to thrive, the media will limit the power your beneficial bacteria has to fully complete the nitrogen cycle.

In order to understand this concept, let’s think a moment about how the nitrogen cycle works: When your fish are swimming around and eating what you feed them and producing waste, all this organic matter breaks down and decays in the tank, creating ammonia. The beneficial aerobic bacteria (or bacteria that do require oxygen) consume the ammonia and convert it into nitrite. These same aerobic bacteria will also consume the nitrite and further convert it into nitrate. Besides adsorption by plants as a nutrient, the only naturally occurring way to remove these nitrates is with anaerobic bacteria, and if your bio-filtration media doesn’t provide small enough spaces for these bacteria to flourish without oxygen, your aquarium will begin to see an increase in nitrates, which are harmful to your fish and tank as well.


Proper Bio-filtration will help reduce aquarium maintenance

If your bio-filtration media do provide these extremely small, low-oxygenated spaces, then the anaerobic bacteria will be able to break down nitrates, converting them to nitrogen gas which won’t harm your fish and will escape the tank as a gas on its own fully completing the nitrogen cycle. With plastic bio-balls, on the other hand, since the nitrogen cycle can’t be completed and you’re left with nitrates, extra measures need to be taken to remove the nitrates, like water changes and pricey, complex filtration setups.


Can CerMedia Help?

Cermedia LLC, located in Buffalo, NY, manufactures MarinePure® Bio-Filter Media, which is a man-made ceramic bio-filter media that has the unique combination of a large amount of surface area for beneficial bacteria to grow in addition to a network of open-flow pores. These features enable water to move easily throughout the part, allowing the nitrogen components to find the bacteria-, allowing all parts of the nitrogen cycle to take place, including ammonia and nitrite elimination and nitrate reduction. MarinePure also does not need to be cleaned, there will always be open pores, as long as there is mechanical filtration pulling out the large particles before they encounter the MarinePure bio-filter media.


If you have any questions about how to access MarinePure® Bio-Filter Media or incorporate into your new or current tank, feel free to reach out to us. We’d love to help walk you through how to use this bio-filter media for a cleaner, easier-to-manage fish tank.

High Surface Area MarinePure Spheres


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