How to Clean Pond Filter Media (And Optimization Tips)

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Guide to Cleaning & Optimizing Pond Filter Media 2022

koi pond filter cleaning
Pond fish require a clean and efficient filtration system to remove harmful waste substances from water. Public domain.

In an ideal world, pond filters would never need to be cleaned as they would be entirely self-sufficient. Without debris, the mechanical media wouldn’t become clogged or damaged, and in low bio-load conditions, the biological media would be self-cleaning via its own beneficial bacteria populations. Sadly, this isn’t always the case in reality, and most pond filters would benefit from a clean every now and again to keep them in good shape. This is especially true if you have fish in your pond, as a good quality filtration system is vital for optimal fish health.

Even though you likely can’t escape the cleaning duties when it comes to pond filters, you can certainly try to reduce the cleaning required by making sure your filter and media is performing optimally. A filter that is constantly becoming clogged or not filtering out particles may need to be replaced, as the filter could be too small for your bio-load (waste level) or the media itself could be damaged. In most cases, filter media should only need to be cleaned a few times a year, so if you find yourself having to unclog your filter more often, it may be time to review your options.

Contrary to popular belief, both mechanical media and biological media should be cleaned if they become completely clogged with debris and “gunk.” Just like mechanical media, bio-media cannot perform efficiently if it becomes covered in debris, and the beneficial bacteria living there will suffer. It’s a little more difficult to know when bio-media is in bad condition, but tell-tale signs include changes in water clarity, strong odours, and even sick pond fish!

How often should I clean pond filter media?

koi pond filter box cleaning
A filter box should rarely need a clean if the pond is well maintained and the media is performing optimally.

A well optimised and maintained filter should only need a clean a few times a year, but the amount of cleaning would also depend on your pond’s bio-load. In general, a filter should be cleaned as soon as you notice a drop in water flow from the filter outtake, as this is a good indicator the mechanical media is becoming clogged. In terms of bio-media, it’s a bit more difficult to determine, but changes in water clarity, a buildup of sludge, a strong smell, or newly sick fish may all be indicators that your biological media is under-performing.

The only way to find out for sure is to open up your filter box and have a peek inside at the media! You should be able to instantly tell if your mechanical media is blocked, as they’ll have a thick layer of debris covering the fronts of the pads and also between the different layers.

In terms of biological media, if you notice they’re covered in a thick layer of green/black “gunk”, they may require a clean alongside the mechanical media. Bio-media will go brown in color over time as beneficial bacteria colonise the surface, and this is totally normal and not an indicator they’re dirty. You need to be careful with bio-media, as cleaning should only be a last resort if they’re covered in debris and the bacteria cannot perform their function.

Will cleaning kill beneficial bacteria? Can I use tap water?

A common misconception is that you should never clean biological media as this would also remove the beneficial bacteria that live there. While it’s true cleaning with mains water (chlorine) can remove beneficial bacteria, it may still be necessary if the media is totally clogged.

Aerobic beneficial bacteria require oxygen to function, and they will not be getting any oxygen if they’re covered in debris and waste buildup. The only bacteria which will function here are slow-digesting anaerobic bacteria which may make your filter smell like rotten eggs as they release hydrogen sulphide and consume CO2. As well as this type of bacteria, harmful strains of bacteria which are dangerous to both fish and humans can breed in low oxygen conditions, so often it’s better to simply clean the bio-media and start again. If your beneficial bacteria cannot work due to the condition of the media and filter, they’re no better than having no bacteria at all!

If you do clean your bio-media, which we still only recommend if they’re covered in heavy debris, you can always top up with beneficial bacteria supplements to kick-start your populations again.

Why does my pond media keep getting clogged?

how to remove debris from fish ponds
Filter boxes should have different layers of mechanical media to reduce clogging and improve debris removal.

If you’re cleaning your filter regularly due to the media becoming clogged you may need to upgrade your filter box or optimize the media!

One of the most common reasons filter media becomes clogged is due to the filter itself being far too small for the pond’s bio-load and waste levels. This is a dangerous situation to be in if you have fish, as without sufficient filtration to remove waste substances, such as ammonia, they can grow to harmful levels. Making sure your filter box is big enough for your pond is important, and it’s always better to over-filter water with fish than under-filter. If you’re unsure of which two filter boxes to buy for a pond, you can safely pick the larger one to ensure the best performance.

If your filter is the correct size, your media could be damaged, worn out, or need replacing. Regular media can also be switched out to a more optimized variety, as some basic media which comes with filters can be underwhelming. Making sure your bio-media is optimized with a high surface area for beneficial bacteria colonization and having several layers of mechanical media with differences in porosity will help catch all types of debris. If you only have a single filter pad which is quite fine, it’s likely becoming clogged because all debris, big and small, are getting stuck to the single surface – it should be spread over several layers!

How to Clean & Optimize Pond Filter Media

1) Cleaning Mechanical Pond Media

mechanical pond media filter sponges
Mechanical media can be cleaned with tap water, and the more layers the better for filtration!

Mechanical media, such as sponges or filter pads, can be easily washed using regular mains water from your garden hose. This type of media is designed to trap debris particles, and is not optimized to house beneficial bacteria, so regular tap water is perfectly fine to use. Usually, you’ll find if you have several layers of media, the finer pads will become clogged first and will need the most thorough clean. This is normal as the finer the porosity of the filter media, the wider range of particles it can collect, so don’t worry if some layers are much dirtier than others.

Making sure to give the media a very good clean, removing debris manually, and squeezing out smaller particles is recommended before placing back in the filter box. Unless you have really heavy debris in your water, you should only need to clean mechanical media every 3-6 months.

Ways to Optimize Mechanical Media:

  • Make sure you have several layers of media with different sizes of porosity for maximum debris removal.
  • Even though mechanical media is not designed for bacteria, they can still grow here, so a media with a higher surface area can help bio-filtration.
  • Overcleaning is better than under cleaning, as mechanical media performs better when no debris is left over to slow water flow.
  • For more information on good media choices, check our full guide on this here.

2) Cleaning Biological Pond Media 

biological pond media cleaning
Bio-media that becomes clogged should also be cleaned, but adding better optimised media can prevent this from happening.

Biological media, such as bio-balls or ceramic rings, should only be cleaned if they’re totally covered in debris and “gunk.” Bio-media will slowly change color as beneficial bacteria colonize, and it is normal for older media to look brownish in color. This change of appearance doesn’t mean it’s dirty, it actually means it’s healthy! Bio-media will only ever need a clean if the media is completely covered, as this prevents oxygen from reaching bacteria on the surface, which they need to survive and carry out their job.

Beneficial bacteria require oxygen, so if your media looks to have large amounts of thick buildup, you should probably either replace it or clean it. If the media is not thick with debris and simply discoloured, it DOES NOT need cleaning! This means your media and bacteria is healthy and performing optimally in your filter box.

If the media is clogged, cleaning with regular tap water is fine (or you can use de-chlorinated water), as there likely won’t be any beneficial bacteria left under these low-oxygen conditions, anyway. It’s better to remove all the gunk and start again or just replace the media if things get to this stage. After a clean, topping up with a beneficial bacteria supplement will help kick-start your population again.

Ways to Optimise Biological Media:

  • Bio-media that is becoming clogged is likely due to other problems, such as algae, insufficient aeration, or a filter box that is too small for the bio-load. These need to be looked at before replacing media or it will just become clogged again.
  • Adding more optimized bio-media can help with harmful substance breakdown, so you can try a different variety and test the results.
  • Supplementing with beneficial bacteria can provide new media or under-performing media a boost in filtration.
  • Never overload your filter box with bio-media, as there needs to be water flow and movement for oxygen to reach the bacteria and also for dead bacteria to drop off the media.
  • For more information on good media choices, check our full guide on this here.

3) Using Chemical Filter Media (Activated carbon)

activated carbon pond filter
Activated carbon doesn’t need cleaning, and helps to remove heavier organic pollutants, such as chlorine.

A third stage of filtration that doesn’t come as standard in filter boxes is chemical filtration, usually in the form of activated carbon (charcoal). This can be added on top of the regular 2-stage filtration to help neutralise heavier organic pollutants that bio and mechanical media cannot remove from water.

Activated carbon can remove residue chlorine, pesticides, tannins (color), or even leftover medicines or treatments. If you’re having issues with water clarity that bio-media is not able to remove, adding activated carbon to the filter box may help the issue.  Activated carbon can also help prevent biological media from becoming so easily clogged by neutralising pollutants that would otherwise get stuck on the surface of your bio-media.

It only needs to be replaced every few months and requires no cleaning once added, so is a very low maintenance form of filtration.

Check here for more information on activated carbon and our recommended brand picks.

6 thoughts on “How to Clean Pond Filter Media (And Optimization Tips)”

  1. could you please advise me on how to get the correct filter box for my pond.
    is there a calculation to work out the size.

    Kind regards

    T P

    • Hi Terry,

      This guide may be helpful to you:

      At the bottom it covers the correct size of pump you’d need for the average fish pond, and since a pump almost always needs to match a filter’s flow-through specification, it can also help you determine the actual filter size, too. For example, if you have fish in your pond you’d generally want complete pond water turnover at least once an hour; which means if you have a 2000 gallon pond, a pump rated at a minimum of 2000 GPH (gallons per hour) would be suitable to achieve this. Taking this into account, and depending on the filter (pressurized vs non-pressurized), you can easily spec-up a filter which can handle the 2000 GPH flow of the pump, as filters are often marketed in tiers based on their compatible flow rate acceptance.

      However, this is assuming no additional friction or head in the system, so you may need a slightly stronger pump if you’re moving water long distances or to an elevated filter box. The article above covers all this and should make choosing easier, even with the addition of extra components and head height. Hopefully it’s helpful, but let me know if you need more advise!

      You can also find some of my personal recommendations for fish pond filters here –

  2. We swapped out an old sand filter with a new Aqua Ulima, in the process sand has gotten into the new filter and keeps clogging the valve. How can the sand be flushed from the new filter?

  3. Hi, very interesting, my box filter has those bits of plastic pipe abour 1 and half inches long and diameter, they do get clogged up and their is some stuff clinging to it when I wash them out. Do you think this stuff is old fashioned and I should go for the bio stuff you talk about.

    • Hi Adrian,

      I think you’re referring to ceramic ring media (they look like little sections of cut pipe), which is actually a great media for beneficial bacteria colonisation and biological filtration. Although some modern filters are choosing new kinds of media, such as K1 rings, older ceramic style ring media is still very porous with a huge amount of surface area for beneficial bacteria growth. The only issue you’ll find with this media, and a main reason as to why many new filters come with a lighter kind, is that it’s more prone to clogging and requires more hands-on maintenance to remain efficient.

      For example, K1 rings (when used in a free moving bed/under suitable conditions), will ‘self-clean’ to a degree by shedding dead bacteria and sludge build-up as they’re light and designed to move very freely within the filter. Older, heavier media, such as ceramic rings, still perform this function if there is adequate room and flow, but not with the same efficiently, so you’ll see them clog more quickly and require more regular cleaning.

      With that said, so long as your media is not becoming clogged overnight (which may indicate your filter is not a large enough capacity to handle your ponds bio-load), and you don’t mind the occasional cleaning session, I wouldn’t worry as they’re likely doing their job just fine.

      If you’re worried your filter may be struggling, the easiest way to determine this would be with a water quality test –

      If your water quality test result is showing a higher than normal ammonia reading, your filter may indeed be struggling and you may benefit from a higher capacity model. I’ll link some articles below with recommendations if you’d like to look into this in future!

  4. i have an issue with water clarity – my pond is approx 36000 lt.. filters installed are 2 oase 36 screenex wih110w uv’s. 1 x laguna 17000lt & 1 x 15000 lt p/hr pumps feeding the filters, it also has a large box sitting over the top of the pond containing a multitude of plants (box size @ 10ft x 5ft x 12″ deep) the pumps running @ approx 2000lts p/hr.


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