Specialised Uses For Internal Filters In Marine Aquariums - More Useful Than You Might Think

Welcome to Simple Reefs. On this website, we are dedicated to keeping things simple and saving you money. That’s why we have been discussing freshwater to marine aquarium conversions, as of late. As we dive deeper into that subject, it’s time to look at some specialised uses for internal filters in marine aquariums.

Internal Filters Aren’t a Great Primary Source of Filtration

In a previous discussion, we established why the humble internal filter often falls short as the primary source of filtration for a sumpless marine aquarium. Sure, it’s tempting to include one, given the affordable price and all, as well as the possibility that you have an old one lying around. But internal filters have certain limitations that make their use in the saltwater hobby less than optimal.

Whether it is small media baskets, less capacity to move water and provide decent contact time with the filtration media, or the potential to become nitrate factories due to cumbersome maintenance requirements.

There are far better options to utilise as your main filtration life support system. When compared to the robust biological, chemical, and mechanical capacity of a quality hang-on-back or canister filter, for example, their limitations are clear.

⚠️ Caution: Relying solely on an internal filter for biological filtration in a reef tank can be a big mistake. Their limited media capacity isn’t designed to handle the bioload of a mature saltwater display. Always think of them as a supplemental solution and not a primary one.

But does that mean internal filters have no place at all in the saltwater hobbyist’s toolkit? Absolutely not! If we pivot our thinking away from them being a source of primary filtration and into them being a helpful, specialised, tool. The internal filter transforms from a compromise into a highly effective and affordable problem solver.

Let’s take a look at the strategic applications where these simple devices actually really shine – in other words, specialised uses for internal filters in marine aquariums. I’ve got some very specific experience with this, as well, that I will be relating in just a little. Let’s just say that an internal filter helped revive one of my nano tanks not so long ago.

1. The Temporary Mechanical Filter & Water Polisher

Have you ever wondered how to clear cloudy water in a reef tank after cleaning? Your main filtration system is designed for constant, steady operation. However, certain events can overwhelm it with particulate matter, leading to cloudy water that, frankly, ruins the entire aesthetic of the tank and may even stress coral.

Whether this is due to overfeeding, a bacterial bloom, an algae bloom, or just from blowing out your rocks while cleaning, it can be very frustrating.

⚠️ Caution: Don’t let internal filters become “nitrate factories”. Sponges and floss left too long will accumulate detritus which will rot and release excess nitrates and phosphates. Rinse or replace mechanical media frequently.

While the typical way to deal with this problem would be to just wait it out. This is a perfect short-term job for an internal filter packed with a bunch of filter floss.

When to use it:

• Post-Maintenance: After you’ve scraped algae off the glass, blasted the rockwork with a turkey baster, or done a deep sand bed cleaning, the water column can be thick with suspended detritus that includes uneaten food, dirt, and fish waste.
• Aqua scaping: Adding or moving rocks and sand will inevitably cause a temporary storm in your tank.
• After a “Detritus Event”: Perhaps a powerhead fell and blasted sand all over the place, or you discovered and removed a dead inhabitant which kicked the substrate up into the water column.

How to use it: Instead of the coarse sponge it came with, stuff the filter’s media chamber with fine filter floss or even a polishing pad. Place it in the tank and let it run for a few hours. You will be amazed at how quickly it clarifies the water.

💡 Pro Tip: Always rinse internal filter sponges in old tank water, never under the tap. Chlorine and chloramine will wipe out your beneficial bacteria colony in seconds.

Because you can place the internal filter right at the source of the problem, it wastes no time getting to work. It’s going to pull that dirty water in, trap all the detritus, and spit the water back out nice and clean.

Once the water is clear, remove the filter, discard the dirty floss, and store the unit until it’s needed again. This prevents the collected detritus from breaking down and elevating your nitrates. An internal filter is the perfect tool to deal with this task.

2. A Simple, Cost-Effective Media Reactor

Did you know that using an internal filter as a media reactor is actually entirely possible? Dedicated media reactors are fantastic, but they can be expensive and add complexity to a sumpless setup. Some of them are absolutely massive, too. I have a GFO reactor in my sump and man is it annoying. It doesn’t fit comfortably without getting in the way and it is very cumbersome.

In a sumpless aquarium, a traditional media reactor simply isn’t a realistic option. An internal filter can actually be converted into a simple, in-tank reactor for chemical filter media, giving you targeted control over water chemistry.

When to use it:

• Running Activated Carbon: To remove yellowing compounds (gelbstoff, yep, that is a real word), odours, or the toxins released during coral “chemical warfare” event or from external pollutants like air fresheners or paints.
• Post-Medication: After treating a fish in a hospital tank, a bag of fresh carbon in an internal filter is the most effective way to remove residual medication before it’s returned to the display.
• Targeted Phosphate/Silicate Removal: For combating algae outbreaks, a small bag of Granular Ferric Oxide (GFO) or other phosphate absorbers can be placed inside. The forced flow of water through the media makes it significantly more effective than just passively placing a bag in a low-flow area.

How to use it: Simply remove the stock sponge and filter media and replace it with a small, mesh media bag filled with your chosen media. Internal filters work surprisingly well for this and part of that is down to the way they force the water through such a small space.

While this isn’t apt for decent filtration thanks to the way filter floss obstructs the flow, it works really well for chemical media. The contained, directed flow ensures maximum contact time and efficiency. Again, keep this as a temporary measure and make sure you clean the filter once a week.

3. The Essential Tool for Quarantine and Hospital Tanks

This is arguably the single best application for an internal filter in the marine hobby. Quarantine (QT) and hospital tanks are, by nature, simple and temporary setups. But you might be wondering how to cycle a quarantine tank quickly.

Well, an internal filter is a perfect match for your needs. You don’t want to get too complicated and internal filters keep it simple. All you need is a piece of sponge or filter material that has already been seeded with beneficial bacteria by living in your main tank.

💡 Pro Tip: Keep a spare filter sponge or some rubble in your sump or display tank at all times. If you suddenly need to set up a quarantine or hospital tank, you’ll already have a seeded filter material ready to go, no waiting for a cycle.

• Instant Biological Filtration: The filter’s sponge can be “seeded” by running it in the sump of your established display tank for a week or two. This populates it with beneficial bacteria, providing an instantly cycled, ready-to-go biological filter for your QT. Some internal filters might even allow enough space for some well established rubble from your tank.
• Simplicity: No need for complex plumbing. Just attach it to the glass, and it provides filtration, water oxygenation, and water movement in one compact unit.
• Medication Management: As mentioned above, it’s the perfect vessel for holding carbon to remove medications after a treatment regimen is complete.
• Gentle Flow: The flow is often less aggressive than a standard powerhead, which is ideal for fish that are stressed, sick, or recovering. With no substrate or rocks to divert the flow, a lot of filters would blow the fish all over the place. An internal filter simply won’t do that.

💡 Pro Tip: If you’re running medication in a quarantine tank, remove any carbon or chemical media from the internal filter. Carbon will strip the treatment right out of the water.

4. Supplemental Flow & Dead Spot Elimination

Let’s be honest, every reef keeper dreads “dead spots”, areas of low flow where detritus accumulates. They can lead to algae growth and cyanobacteria outbreaks. I absolutely hate seeing those little brown patches on the substrate. While a powerhead is the typical solution, an internal filter offers a dual-purpose alternative.

⚠️ Caution: Strong internal units can create uneven flow patterns. Corals may suffer if the outflow is directed right at them, so experiment with placement to avoid blasting sensitive species.

By tucking a small internal filter behind a rock structure or in a back corner, you not only eliminate a dead spot but also gain an opportunity. You can use that filter for any of the purposes listed above – run a small bag of carbon, some GFO, or just use the sponge for extra mechanical filtration in a problematic area. The one thing to remember is to pull the filter out and give it a clean once a week.

5. Tiny Tanks (Ultra Nanos and Picos)

Certain aquariums, very small nanos and desktop picos for example, simply don’t have the space to accommodate any kind of external filtration. In this situation, an internal filter will be a much better option than no filtration at all.

Pro Tip: When using an internal filter in a nano or pico tank, treat mechanical media like filter floss as disposable. Replace it every few days rather than rinsing and reusing; this prevents nutrient build-up that can fuel algae outbreaks.

⚠️ Caution: Internal filters take up valuable space inside the tank. In smaller nano reefs and picos, that footprint can limit aqua scaping options or reduce swimming room for fish. Plan your layout before dropping one in.

Purchasing a suitably sized sponge or internal filter should give you the opportunity to, not only, filter the water but also create some additional flow.

6. Breeding Tanks

This is one I definitely have experience with. If you are breeding fish or shrimp, you are going to want filtration that isn’t going to have them fighting for their very lives. Anything too powerful will suck them right in and inevitably result in their deaths.

💡 Pro Tip: Don’t overlook aeration. Internal filters provide gentle flow and boost oxygen exchange, which is crucial in smaller, breeding, or heavily stocked temporary tanks.

My Bangaii Cardinals had babies a number of times. Each time, I transferred them to a smaller tank with an internal filter. Thanks to the adjustable flow of the filter, I could create gentle movement that would filter the water without being a hazard. Internal filters tend to have smaller gaps in the actual housing, as well, which can prevent small creatures ending up inside.

7. Coral Quarantine or Holding Tanks

Have you ever tried to attach a Discosoma coral to a frag plug? If you haven’t, I can tell you for nothing that it is incredibly annoying. Any significant flow and that thing is going to find its way off the plug and into the water column.

💡 Pro Tip: Position internal filters near the tank bottom in frag or holding tanks. They’ll help keep detritus suspended so corals and frags aren’t smothered in waste.

⚠️ Caution: Strong internal units can create uneven flow patterns. Corals may suffer if the outflow is directed right at them, so experiment with placement to avoid blasting sensitive species.

If you are keeping coral in a holding tank, a fragging tank, or a quarantine tank, An internal filter can be a much better option as the flow is far more gentle. You can adjust the filter and tailor it to the needs of the coral, preventing them getting blown around.

8. The Targeted Problem-Solver: Using Integrated UV Sterilizers

While the previous points cover mechanical and chemical filtration, some internal filters offer another layer of utility: an integrated Ultraviolet (UV) steriliser. This is where some of my experience with internal filters comes into play.

A full-sized, plumbed-in UV system is a significant investment in space and money. Hell, in a small tank, it might not even be a reasonable possibility. However, a small internal filter with a built-in UV bulb can become an affordable, targeted tool for handling specific biological issues circulating in the water column.

This transforms the filter into a temporary “seek-and-destroy” unit for microscopic pests. If you have spent any time in the hobby, you have probably, at some point or another, wondered how to use a UV steriliser for dinoflagellates.

I actually dealt with a nasty case of Dinoflagellates by doing just this. I blacked out my nano tank, slapped in an internal filter with an integrated UV bulb, and waited patiently for a few days. When the process was complete, the problem was gone and never came back.

It was much cheaper than specialised solutions that can be hard to find in the UK, as well. Just keep in mind, this is a tool and not a cure for problems like parasites. You should always quarantine your fish and treat problems when they arise.

When to use it:

• Parasitic or Bacterial Outbreaks: When dealing with free-floating stages of parasites like Ich (Cryptocaryon irritans) or Marine Velvet (Amyloodinium ocellatum), a UV steriliser can help reduce the number of infectious organisms in the water, lowering the overall stress on your fish. It’s a great choice for using in a hospital tank with a sick fish. Just make sure the UV is turned off during treatment, as per the medication’s instructions.
• Algae or Dinoflagellate Blooms: This is a key application. Many troublesome dinoflagellate species have a stage where they are motile and free-swimming in the water column. Running a UV steriliser can effectively kill these free-swimming cells, helping to break the life cycle and manage an outbreak without resorting to chemical treatments. 🦠 Combine the treatment with a full blackout for even more success.
• “Green Water” (Phytoplankton Blooms): As mentioned earlier, yellow or green water can be caused by suspended algae. A UV steriliser is exceptionally effective at eradicating it by killing the phytoplankton cells as they pass through the unit, leading to crystal clear water often within a few days.

💡 Pro Tip: Some internal filters include a built-in UV steriliser, and they can be surprisingly effective at reducing dinoflagellates, green water, or bacterial blooms. They won’t cure the underlying imbalance, but when paired with proper nutrient management and good husbandry, they can make a noticeable difference in water clarity.

⚠️ Caution: UV sterilisers should be treated as a support tool, not a permanent solution. Over-reliance can mask deeper issues in your tank, so always address the root cause alongside using UV.

How to use it: This is the simplest way to deploy UV sterilisation. You place the all-in-one unit directly into your display tank. There’s no plumbing or extra pumps required. You can run it 24/7 during an outbreak and then easily remove it once the issue is resolved.

You can even adjust flow rate to target specific nasties. This approach provides the benefits of UV on a temporary, as-needed basis without the cost and permanent installation of a larger system. It’s a great example of using an internal filter as a precise solution for a specific problem.

9. Temporary or Emergency Filtration

You may be wondering what to do if my aquarium filter stops working? A frustrating reality of owning a delicate marine aquarium complete with coral and exotic fish is how important it is to have backup equipment. Heaters fail, pumps fail, lights fail, and, yes, filters fail too. Having an internal filter as a backup form of filtration is a great way to prepare for the worst.

Should an external pump fail or should your current filter stop working. An internal filter can be used as a stop gap filter until you can replace the one that broke. It will help clean the water while also providing some additional flow and extra water oxygenation. All without breaking the bank, too.

To Summarise

So to wrap all of that up into one easy to check list. While not recommended as a primary filtration source for a display tank, an internal filter becomes an invaluable and affordable tool when used for specific, targeted tasks. Here are the best applications:

1. Temporary Water Polishing: To quickly clear cloudy water filled with suspended particles after maintenance, aquascaping, or cleaning the rocks and sandbed.
2. Simple Media Reactor: As a cost-effective, in-tank reactor to run chemical media like activated carbon (for clearing water or removing toxins) or GFO (for phosphate removal).
3. Quarantine & Hospital Tanks: To provide simple, reliable, and instantly “cycled” filtration (by seeding the sponge) in temporary setups for new or sick fish.
4. Supplemental Flow & Dead Spot Elimination: To provide water movement in low-flow areas of the tank, with the added benefit of holding mechanical or chemical media.
5. Primary Filtration for Pico & Nano Tanks: For very small tanks where space limitations make larger hang-on-back or canister filters impractical.
6. Breeding Tanks: To offer gentle, adjustable filtration that provides necessary circulation and oxygenation without harming or sucking in delicate fry or shrimp.
7. Coral Holding & Frag Tanks: To create gentle flow suitable for sensitive corals or newly made frags that could be damaged or dislodged by strong currents.
8. Targeted Problem Solving (with UV): Using a model with an integrated UV steriliser to combat specific water column issues like dinoflagellate blooms, green water, or the free-swimming stages of parasites.
9. Emergency Filtration: As an inexpensive and easy-to-deploy backup to provide temporary filtration, flow, and aeration if your main filter system fails.

When it comes to internal filter usage in a marine aquarium, the key is to shift your perspective. Don’t view an internal filter as a failed primary filter; see it as a versatile, multi-purpose tool that can get you out of a bind or even be utilised to target very specific problems.

It’s the perfect tool for temporary tasks, specialised applications, and supporting secondary systems like quarantine tanks. So, before you lob that old internal filter that’s probably collecting dust into the bin, consider the strategic roles it can play. It might just be the simple, effective solution you’ve been looking for. Thanks for reading and spending your time at Simple Reefs.