How To Change An Aquarium Filter Without Losing Bacteria

    How To Clean An Acrylic Tank

    How To Change An Aquarium Filter Without Losing Bacteria

    changing fish tank filter sponge

    Just the fact that you’re wondering how to change an aquarium filter without losing bacteria means that you’re way ahead of the game! A lot of first-time fishkeepers will dive in head-first when getting their first tank, without researching aquarium cycling or how maintenance should look like.

    A big part of your tank maintenance routine will revolve around keeping the established bacteria in your tank in order not to send your aquarium into shock. That’s why learning basic maintenance should come first, before picking out all the gorgeous critters and aquascaping goodies.

    When you cycle a tank, the filtration system is the first place where beneficial bacteria will set and start accumulating. Nitrifying bacteria (good bacteria!) has a vital role in turning your tank into a thriving habitat for plants & fish alike.

    You can see why learning how to change a fish tank’s filter without losing bacteria should be part of “Fishkeeping 101” for any aquarist.

    Here’s a list of filter-changing options that will protect the established nitrifying bacteria in your tank:

    Change tank filter sponges one at a time.

    Filters work by trapping debris and particles while circulating water. Depending on how dirty the water in your tank is, the filter media that water passes through will eventually become clogged and prevent the filter from working efficiently.

    If your filter’s filtering media includes two sponges (highly recommended!), you should only change one of the sponges and use the remaining sponge along with a new one.

    This process allows the developed bacteria that’s set up camp in the sponges to have time to colonize the new sponge. There are enough good bacteria on a single sponge to prevent your tank’s water quality from dropping when changing the filter media.

    If your filtering system only comes with one sponge, you can try cutting it in half, and pairing an old half-sponge with a new half-sponge to mimic the same process.

    Leave the old filter in the tank.

    If you’re changing your tank’s entire filtering system, you should definitely plan on keeping both the old and the new filtration systems in the aquarium until the colony of beneficial bacteria has time to settle in the new filter.

    This set-up is temporary, easy to implement, and very efficient. Keep the old filter while running the new filtering system for 4 to 6 weeks, and you’ll be able to make the switch with virtually no bacteria loss.

    It might not be the quickest way to change an aquarium filter without losing bacteria. Still, it’s definitely the least expensive method to use when switching to an entirely new filtration system.   

    Reuse the filter media from the old filter.

    If keeping two filtering systems in the same tank just isn’t feasible for your set-up, the next best thing you can do is to reuse the filter media from the old system in your new filter.

    Granted, this will work best if the two filtration systems have similarly sized and shaped media. If you’re working with filtering cartridges, and you’ve bought an upgraded filter or switched brands, this might be a bit trickier.

    As long as the old filter cartridge is in good shape and not falling apart, you can reuse it for 4 to 6 weeks in the new filter. During this period of time, your new filtering system might not work at its full potential (given the old cartridge), but it will benefit your tank’s culture of nitrifying bacteria greatly.

    This method will give bacteria time to grow and colonize the new filtration system, preventing the risk of your aquarium developing “new tank syndrome”, just because of a filter change.

    A drastic loss of bacteria, paired with an immature (uncycled) filtering system, can wreak havoc in any tank. That’s why waiting 4 to 6 weeks to fully switch to the new filter is definitely worth it.

    Always clean filter media in old tank water.

    This filter maintenance step has more to do with cleaning filter media rather than changing it. But it’s a fishkeeping rookie mistake that can cost you some good bacteria and sometimes even the life of a few pet fish.

    Always clean filter media in old tank water, outside the aquarium, with a gentle touch. The goal when cleaning filter media is to remove clogged up waste and debris.

    Nitrifying bacteria isn’t something that’s supposed to be cleaned or removed. Even a simple rinse under tap water (which is chlorinated) can result in your tank’s culture of bacteria taking a huge hit.

    Bacteria IS your cleaning crew (more on this later!), so all you need to do when cleaning filter media is to make sure water can pass through it during filtration.

    Consider a 3-stage filtering system.

    A 3-stage filtering system will allow you to change/clean the filter media without ever having to worry about losing bacteria.

    Here’s what this type of filtration system typically includes:
    Mechanical media – pre-filter ceramic coils/rings;
    Biological media – coarse/finer sponges;
    Chemical mediaactivated carbon.

    Bacteria will grow and accumulate on all of these filtering media, giving you the chance to change/clean each component separately, without disrupting the colony of bacteria in your tank.

    You will have to keep track of which filter media you changed last, before choosing to clean or change another. This gives bacteria time to grow on the new media in-between changes.

    Give each element at least 6 weeks to mature and get covered by nitrifying bacteria.

    This filter maintenance method does require a bit of pre-planning, but it’s the best long-term solution for your bacteria preservation efforts.

    If there’s a sudden increase in waste or debris clogging up your filter, and weakening water flow, and affecting oxygenation, don’t hesitate to clean it.

    Nitrifying bacteria might have settled in the filter first, but it’s not the only place where it’s growing in your tank.

    See how to change an aquarium filter without losing bacteria here:

    How To Clean A Tank Without Losing Bacteria

    how to clean a tank without losing bacteria
    Ember tetra (Hyphessobrycon amandae)

    You can find unlimited resources online on how to clean an aquarium, but here’s how you shouldn’t clean it if you want to avoid losing beneficial bacteria:

    Don’t deep clean a tank!

    Water changes, siphoning gravel, changing filters, and other tank maintenance activities are all important, but they are not meant to be done all at the same time (unless the tank’s condition is unsalvageable).

    The balance in your aquarium’s bacteria culture relies on you to perform small and gradual routine cleanings, rather than one deep-cleaning fiasco.

    You should always alternate maintenance-related activities, giving the bacteria in your tank plenty of time to re-settle and colonize the new media (filtering media, décor items, gravel, new gear, etc.).

    Why is deep-cleaning an aquarium detrimental to an established culture of nitrifying bacteria?

    • Deep-cleaning will cause a bacterial imbalance strong enough to cause a drop in water quality.

    Nitrifying bacteria turn toxic nitrites and ammonia into non-toxic nitrates that help plants grow in a tank. Anything that gets in the way of this all-important nitrogen cycle will have a negative impact on your tank’s water quality.

    Whether you remove, clean, or change too many elements in your aquarium, a sudden bacterial imbalance will leave your tank vulnerable to ammonia poisoning.

    • Deep-cleaning a settled gravel bed will disrupt well-established bacteria.

    Good bacteria tend to settle and grow on the upper layer of your tank’s gravel.

    Siphoning the gravel immediately after performing another type of maintenance will put your tank at risk for a major bacterial imbalance.

    Although nitrifying bacteria makes its way onto most surfaces within a tank, re-colonizing siphoned (or washed!) gravel takes a lot of time.

    With bacteria only developing at a certain rate, your aquarium’s water can become toxic for all of its inhabitants in the absence of well-established bacteria.

    • Massive water changes (70% or more) will remove most free-floating bacteria.

    Regular maintenance water changes should range anywhere between 10-25%, performed every two weeks. There is a reason why small and frequent water changes are the standard practice for most aquarists.

    While deep-cleaning a tank, you’ll most likely dislodge a lot of debris, which will turn the water cloudy. This is when inexperienced fishkeepers do massive water changes to get their tank’s water to be crystal clear again.

    The reality is that you’re not cleaning the cloudy water; you’re just removing most of the free-floating beneficial bacteria from your tank. A practice that will 100% backfire!

    How Do You Get Good Bacteria In An Aquarium?

    how often to change biological filter media
    School of Bronze corydoras (Corydoras aeneus) swimming in aquarium tank.

    Aquatic nitrifying bacteria will naturally build up on your tank’s filtering system when first cycling an aquarium.

    Other surfaces where good bacteria will settle and accumulate in a cycled tank are:

    • the glass walls;
    • filter media;
    • live/artificial plants;
    • decorations;
    • gravel.

    You can add more beneficial bacteria to your tank by giving the existing culture of nitrifying bacteria in your tank the right conditions to reproduce quicker:

    • slightly increase the water temperature inside your aquarium;
    • keep the lights off;
    • keep the filtering system running;
    • hold off on adding more fish;
    • add extra filter media;
    • introduce an additional oxygen supply source (air pump/air stone).

    Why Do You Need Bacteria In Your Tank?

    replacing filter cartridge in an established aquarium
    Bumblebee Goby (Hypogymnogobius xanthozona)

    A well-established and balanced culture of nitrifying bacteria will work as your tank’s live biological filtering system. Beneficial bacteria will help keep your water clear and prevent toxic ammonia & nitrites from accumulating.

    Some bacteria will consume leftover fish food and waste, dead plant material, and organic debris.

    Other bacteria will use ammonia and nitrates to feed on. This is what aquarists refer to as the “nitrogen cycle”. This cycle follows a certain pattern to help purify the water in your aquarium:

    • fish eat food;
    • fish produce waste fish waste, leftover food & plant matter break down into ammonia;
    • nitrifying bacteria turns ammonia first into nitrites and then into nitrates;
    • nitrates are kept at a safe concentration level through regular water changes and by serving as food for live aquatic plants.

    High levels of ammonia and/or nitrites in an aquarium can be detrimental and sometimes even fatal for fish. Preserving the culture of nitrifying bacteria in your tank is the best way to keep your fish happy, healthy & thriving!

    What Happens If You Lose All The Bacteria?

    how to swap aquarium filter
    Colorful Gold, Yellow Molly (Poecilia sphenops).

    Changing your aquarium’s filter without losing bacteria is important because it will prevent you from causing a bacterial imbalance in your tank during routine maintenance procedures.

    But the truth is that you won’t ever lose all the good bacteria in your tank, especially not by doing regular aquarium maintenance.

    Nitrifying bacteria in a cycled healthy tank is established enough to allow for a safe filter change without you fearing a biological crash.

    What Else Can Kill Good Bacteria In A Tank?

    how to change aquarium filter without losing bacteria

    Don’t feel like you’re solely responsible for your tank’s bacterial balance. There are quite a few external factors that can kill nitrifying bacteria, which are out of your control.

    Dosing fish medicine in an aquarium is one of the main culprits that goes unnoticed when there’s an unexpected drop in water quality.

    Power outages that cut-off your tank’s oxygen supply can wipe out a substantial part of your aquarium’s bacteria culture.

    The nitrogen cycle, during which bacteria turns ammonia/nitrites into nitrates, needs oxygen to take place. Dangerously low oxygen levels can starve off a well-established culture of nitrifying bacteria in just a few hours.

    How To Tell If You Have Enough Good Bacteria In Your Tank

    Guppy, poecilia reticulata
    Guppy (Poecilia reticulata)

    The best way to check and monitor whether your tank and its filtering system have developed a mature culture of bacteria is to regularly test the water using aquarium test kits.

    Bacteria won’t be visible to the naked eye, and even clear water can be deceiving. Crystal clear tank water could still cause ammonia poisoning and kill fish, without any tell-tale signs that your bacterial balance is off.

    The most important water parameters you should be testing for in an aquarium are:

    • pH level

    You’ll need to monitor the pH level in your tank to make sure it stays within the recommended range for the fish you have living there.

    Typically, a pH ranging between 6.0-7.5 is okay for tropical fish, while saltwater fish will need the pH level to fall somewhere between 8.0-8.4.

    Keeping the pH level in your tank stable is more important than “chasing” the perfect pH level.

    • Ammonia

    If you have a mature culture of nitrifying bacteria in your tank, the ammonia level should be at 0.

    • Nitrite

    Same as with ammonia, when testing the water, nitrites should be at 0.

    • Nitrate

    Nitrates are non-toxic in small concentrations, but their level should fall somewhere below 20ppm if your tank has a good bacterial balance.

    If your test kit shows a higher concentration of nitrates, avoid adding more fish for a while, and add live plants to your aquarium.

    Fishkeepers can use ammonia removers, water conditioners, and store-bought live nitrifying bacteria to balance out any of these levels.

    There’s rarely a need to add store-bought bacteria to a cycled tank.

    How Often Should You Clean The Filter?

    how to change aquarium filter without losing bacteria

    Cleaning your tank’s filter should be a multiphase process in order to avoid sending your tank into “new tank syndrome”, which can happen if you remove too much nitrifying bacteria.

    Clean filter media in a container of siphoned old tank water, trying to only remove waste and debris.

    Try to clean filtering media alternatively, without ever deep-cleaning a filtering system all at once.

    You should perform this filter maintenance routine every 4 weeks in a cycled tank with a well-established culture of beneficial bacteria.

    Cleaning aquarium filters too often can have a paradox effect, as your tank’s water will get dirtier quicker (and even turn toxic) due to the disturbance in the bacterial balance caused by the cleaning process itself.

    How Often Should You Change The Filter?

    how often to change filter cartridge in fish tank
    Kuhli Loach (Pangio kuhli)

    When talking about changing the aquarium filter without losing bacteria, the change refers to the filter media used by your filtering system to trap particles of waste and debris.

    Filter cartridges should be changed at least once a month. The frequency of filter changes will depend on a lot of things that are particular to your tank’s set-up.

    Apart from a monthly filter maintenance session, you should change filter media when the water flow becomes noticeably slower all of a sudden.

    If you notice that your tank’s filter seems to be under-performing, check to see if the filter media hasn’t become clogged-up with waste/debris.

    If the filter isn’t performing better after changing filter media, you can assume the filtering system is malfunctioning, and it’s time to start looking for a replacement.


    how to change aquarium filter without losing bacteria
    Red Cherry Shrimp (Neocaridina davidi)

    Nitrifying bacteria are a fishkeeper’s best friends!

    The biologic filtration process relies on your tank having a well-established culture of beneficial bacteria, and it’s your job to minimize bacterial imbalances.

    You now know how to change an aquarium filter while keeping the beneficial bacteria, but more importantly, you know that doing filter maintenance won’t make or break your tank’s bacteria culture.

    Small, gradual, or partial maintenance activities performed on a schedule will make it easy for you to sustain an aquarium’s biological balance.

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