Fully draining pond water should always be a last resort, and it’s certainly not something you need to do if you want to clean your pond. As a matter of fact, draining your water can actually make the pond dirtier in the future as the natural ecosystem will be disrupted, especially in wildlife ponds. Even though heavily draining water may be required under some circumstances, in terms of general cleaning, it is rarely a necessity so long as you have the right equipment at hand.
A common misconception among some pond owners is that “dirty” water needs to be drained before ponds can be properly cleaned. In fact, the opposite is often true, with water that appears dirty actually being very healthy and working with the pond’s eco-system to provide a natural cleaning service.
Pond water is filled with micro-organisms and millions of beneficial bacteria which are constantly at work to break down harmful substances, such as ammonia and nitrites. These are essential to ponds with fish, and form the basis of the “nitrogen cycle,” which helps keep the pond in balance.
Removing pond water means you’ll also be reducing the natural beneficial bacteria populations, which will cause a reduction in your pond’s biological filtration process. Topping up with more water after draining can cause even more disruption, as mains water is usually high in chlorine, which is toxic to much of the natural micro-organisms living in ponds.
Cleaning a pond without draining will ensure that your natural bacteria populations are maintained, allowing them to continue providing bio-filtration after the worst of the waste is removed. If waste levels get too high, you will just need to manually remove enough waste so bacteria can get back to work again – no total drainage required!
How to Clean a Pond Without Draining it
Step 1) Skim the Surface for Floating Debris
- POND SKIMMER Removes debris from the water’s surface before it sinks
- PRE-FILTER Helps protect your pond pump from clogging
- EASY TO INSTALL AND CLEAN Draws in water and collects debris in a basket and replaceable filter pad
The first thing to clean in a pond is any floating surface debris, as this will eventually sink and contribute to sludge at the bottom of the pond floor. Removing as much floating debris as possible is always better before cleaning the pond liner or you’ll just be cleaning it again later as it sinks. Floating debris includes things like leaves, sticks, twigs, and dead insects or larvae. These can be removed manually using a basic pond net, or you can make use of an automatic skimmer system for constant clean-up.
If you’re going for a pond net, make sure to pick one up with a wide basket opening and a fine mesh so you can catch all sizes of debris easily. Pond skimmers are a good long-term solution if you’re constantly fighting back debris that falls into your pond, or if you have lots of fish and want maximum water clarity. Box skimmers will work to clean the water surface quickly and have a high capacity for larger ponds, whereas smaller ponds can benefit from floating or submerged skimmers due to their lower purchase cost.
Unlike nets, skimmers are better long-term investments as they can remove much finer debris which isn’t always easy to see and are also able to work 24/7 to keep the surface clean. If you have a small pond, however, and don’t mind keeping on top of daily cleaning, a pond net should be more than enough!
Step 2) Clean the Pond Floor with a Vacuum
- Max; Suction Depth: 7 Ft
- Suction Hose Length: 16 Ft
- Discharge Hose Length: 8 Ft, Max; Flow Rate: 1300 Gph
The next step is to combat any bottom sludge you have, and although you don’t need to remove it all, it can be beneficial to reduce most of it before winter so your fish have a safer hibernation period. This is often the step where you may feel draining the pond would help, but this is only necessary if you’re manually removing sludge with a net or rake. Another way to remove bottom muck, which is also much faster and easier, is to invest in a quality water vacuum.
Pond vacuums will allow you to clean the bottom of your pond liner without having to drain water, and the best models will have a variety of different head attachments for cleaning hard-to-reach areas of the pond. If you have a particularly deep pond, you’d want to look for a model which can keep suction at good depths and which has an extendible handle for easier cleaning. Basic models will lose suction the deeper you go, and although they may be ideal for smaller ponds, they may not be up to the job of cleaning the deepest points of larger ponds.
On top of this, you’ll want to have a vacuum with a reliable discharge system for constant cleaning and to make it easier to remove waste. The two vacuum models we recommend are the Oase PondoVac 4 and the Matala Power Cyclone, as they include all these features and will work for both small and very large pond builds.
Step 3) Supplement with Beneficial Bacteria
- Contains one (1) API POND ECOFIX SLUDGE DESTROYER Pond Cleaner And Sludge Remover With Natural Bacteria 64-Ounce Bottle
- Contains natural active ingredients to break down fish waste and consume pond sludge
- Breaks down dead algae and digests leaves and grass clippings
After cleaning out most of the bottom sludge, you can then supplement with a natural beneficial bacteria product to help break down any lingering waste. Most sludge remover treatments work using highly concentrated bacteria which is able to break down organic matter throughout the pond. Just like a pond’s natural beneficial bacteria, sludge remover bacteria works in the same way and can help give the natural populations a boost after a deep clean.
If you have a wildlife pond and want to keep most of your sludge, you can instead just add extra beneficial bacteria to complement the nitrogen cycle. Sludge can be beneficial to wildlife ponds as it provides nutrients for plants, as well as food for insects and micro-organisms. Problems with excess sludge occur mainly with fish as a by-product of its natural decomposition is ammonia, which is highly toxic to koi and goldfish. Without any fish in the pond, adding more beneficial bacteria is a cheaper and better way to control sludge in comparison to removing it all with a vacuum.
For more information on the top sludge remover bacteria and how to use them, check our main article on this here.
Step 4) Control & Remove Growing Algae
- Vitronic 18-36W are simple, yet versatile UV Clarifiers designed to operate with all filter systems, although best suited for the BioSmart...
- Easily integrated into an existing or new pond system, Vitronic UV Clarifiers clean the green out of water.
- High quality UVC bulbs guarantee a long service life, and a constant effective irradiation capacity.
Even though algae isn’t technically waste, it should still be controlled and cleaned out so it doesn’t cause issues with water quality and sludge build-up. Small amounts of algae in ponds are actually beneficial, providing hiding spots from predators and making good snacks for goldfish. Problems with algae occur when it’s left to grow uncontrolled and rapidly takes over the pond system. Algae blooms will cause issues with sludge as old plants die and sink to the bottom, with this gradually reducing oxygen content as bacteria work to break down the new waste.
You don’t have to drain a pond to combat algae, and even string algae attached to the pond floor can be removed with the right mix of treatments. To combat free-swimming algae we recommend installing a UV clarifier, which will filter water and destroy algae at the cellular level. For removing deeper string algae that won’t fit through a clarifier, using a pond vacuum will make short work of the nuisance plants.
Algae can also be controlled in the long run by adding more plants to your pond, as they directly compete with algae for nutrients, gradually slowing its growth. For fast control of algae, however, a combination of a UV clarifier and a vacuum should be enough to remove almost all of the plants without the need to drain any water.
Step 5) Clean & Optimize Water Filtration
A final thing to do when cleaning a pond is to ensure your water filtration is the best it can be to reduce future cleaning and maintenance. A pond with a healthy biological filtration system will have few problems with water quality, and a filter with efficient mechanical media will reduce overall debris in the pond. Although filters should be rarely cleaned as they can harm bacteria living in the box, it’s sometimes necessary if the media has become completely clogged. Likewise, mechanical media can become damaged over time and may need replacing every few years to ensure optimum filtration is taking place.
Having an efficient filtration process in place will help reduce overall cleaning and also improve water quality for pond fish. For further information on optimizing water filtration, cleaning, and what equipment to use, see our articles below:
- Cleaning and Optimizing Water Filtration
- Best Filter Media for Ponds
- How to Keep Leaves Away from Pond
- Ultimate Guide to Algae Control
- Removing Duckweed Naturally
Should I Perform a Water Change when I Clean?
Water changes (removing and adding water) may be beneficial in some circumstances, but we never recommend a full pond water change (full drainage) as you’ll be effectively resetting the nitrogen cycle. If you have a heavy fish-stocked pond it can be difficult to maintain water quality as fish produce so much waste, especially in summer when their metabolisms are high.
In cases such as this, performing a small water change during cleaning can help keep ammonia levels down and improve overall water quality. Beneficial bacteria can only do so much and can easily be overloaded in ponds with massive amounts of waste build-up, so water changes can sometimes be a good option for maintaining water conditions.
For ponds without fish, water changes should not be required unless your water quality is particularly poor; which you can determine using a water testing kit. For general cleaning, which includes bottom muck, algae, and floating debris, you should not need to remove any water to get the job done. If your pond water testing shows positive results, removing water may cause a drop in water quality and make it more difficult to maintain cleaner water in the future.
If you do decide you want to perform a water change, however, you should make sure water is safely dechlorinated before adding to the pond or you could have problems later down the road.
When is the Best Time to Clean a Fish Pond?
Although cleaning can be carried out whenever you need to, the best times for fish ponds would be at the start of spring and the end of autumn. Cleaning at the end of autumn ensures waste levels are minimal moving into winter so fish have a more comfortable (and safe) torpor/hibernation period. Leaving sludge and debris in ponds over time can cause all sorts of problems for fish, especially if water freezes over and no gas exchange can take place.
In instances such as this, harmful substances will slowly rise and oxygen content will be reduced, eventually leading to fish becoming sick or dying come spring. Performing a deep clean at the end of autumn is common practice for fish keepers, and should be something you consider if you have koi or goldfish.
Likewise, a small clean can be carried out during spring when temperatures begin to rise and fish become more active. Although it won’t be as large a clean as your autumn one, it is useful to supplement the pond with beneficial bacteria and remove any lingering debris for the best kick-start to the year. Other times when you may need to clean your pond would be to remove algae overgrowth, fallen leaves, or excess plants, such as duckweed.
This tutorial has been very helpful.
Hi Rebecca,
Thanks for the comment. Happy to hear you found it helpful!
What a wonderful tips thanks for the lesson
Hi Markus,
Thanks for the comment! Glad it was helpful to you.
Thank you for the tips. We just bought a house with a pond and are in need of as many tips as we can get.
Hi Caralyn,
Glad to hear you found some of the tips here useful. Best of luck with the new house and pond! Be sure to let us know if you have any questions or need some help along the way.
I too, just bought a house that has a koi pond, and also need all the advice I can get.
I live in Rhode Island, the pond is approximately 15’L x 3’W x 3’D. There are about 12 koi, some as large as 5″. It has a filtration system, which was badly clogged and not functioning when I bought the house, surprisingly no dead fish. I dug into the filtration box, cleaned out the heavy silt, scraped off the pump and motor, washed off the filter. Then at the other end, opened the fountain, cleaned sludge from the pipe. Plugged it all in and viola! Full function filter, pump, and fountain. And thank goodness, no dead fish.
What I’d like to know is how thick of a layer of silt is healthy to have at the bottom of the pond? And if I need to remove, must I use the expensive vacuums? Is it safe for the fish if I dig deep and scoop with a shovel of sorts? Or does that cause too much action of the silt and potentially harm the fish?
Thank you very much, your site is very informative.
Hi Amy,
Congrats on the new house and pond! It sounds you’ve done a great job getting equipment working again, and since there are no sick fish, water quality must still be within tolerable parameters – which is good!
In terms of pond silt (sludge), there is sadly no hard-and-fast rule, and the same amount which may be healthy in one pond may be unhealthy in another. The only way to determine what is right for your new pond is to perform a broad range water quality test; specifically taking note of the readings for ammonia, nitrites, pH and KH. Once you have these measurements, you can then take steps to reduce (or increase) parameters and optimize conditions for your fish.
Personally, I wouldn’t disturb the sludge just yet as this may kick-up harmful substances in the lower layers, which could cause further issues if water quality is already poor. Below is what I would probably do in your situation to determine the current condition of the pond:-
1) Get equipment up and running (which you’ve done!)
2) Perform a water quality test and note all parameters
3) Perform a 25-50% water change (reduces ammonia/nitrites and replenishes KH/Alkalinity)
4) Perform another water quality test and note all parameters
5) If parameters are still not ideal, take further steps (i.e, slowly reduce silt, increase aeration, supplement bacteria)
6) Monitor fish for stress, injury or illness (are they eating? are they dull in color?)
It may take some time for conditions to settle, so if the fish are happy and eating, you could wait 5-7 days after the water change before you re-test water quality. Here are some separate articles that cover these subjects in more depth that may be helpful to you:
https://pondinformer.com/best-pond-water-test-kit/
https://pondinformer.com/koi-pond-water-change-guide/
https://pondinformer.com/how-to-lower-ammonia-fish-pond/
Be sure to let me know if you have any more questions or run into problems. Best of luck with the pond!
I have a tiny pond(?) a black plastic round tub (3.5′ diameter). I have one of those solar fountains that is keeping the water moving. I notice that their is some debris in the bottom of the tub that I am not sure how to remove. Can I use a shop vac? I just love having this in my little garden and trying to have it not become a nuisance. I am in Florida.
Hi JoAnn,
Yes, so long as the vacuum is designed for wet application it should be fine to use. Alternatively, you could also make use of a regular aquarium siphon so long as the tub isn’t too deep.
About 8 years ago we installed a pond with a waterfall in our backyard that has many frogs and well established plants. There are also a few fish (bottom feeders) that we have no idea how they got in there, and only have seen them a few times as the water has become very mucky. It is so bad that we have to change the pond filter media twice a day. My husband wants to remove all the water and clean it. This would have to be done manually as we did not install a drain. After reading your recommendations on this site, I think we would be better off getting a vacuum to clean the muck from the bottom. What do you suggest? Our pond is about 3′ deep and approximately 10′ x 12′. Thank you.
Hi Karen,
If your filter media is becoming clogged that fast with just brown gunk (not green debris – indicating active algae), it sounds like your bottom muck has reached a critical point and you simply have a huge amount of free-swimming debris particles present. In that situation, I agree that a water vacuum would probably be the best (and easiest) way forward. After cleaning the bottom muck out and letting things settle, if you’re still not satisfied with clarity, a few small water changes may be beneficial to further reduce waste substances and top-up natural alkalinity.
Can fish get injured or sucked up by pond vacuum?
Hi Debra,
It’s very unlikely, especially for most adult fish. The majority of pond vacuums have a fairly narrow hose diameter, so unless you have fry or very small fish species (mollies/guppies etc.), I don’t think there would be a problem here. Even if you do have small fish in your pond, vacuums are quite noisy and, in my experience, fish tend to keep away from the area you’re cleaning. Also, vacuums are designed to be used in contact with the pond liner, and since fish don’t actively lay on the bottom, it would be very unlikely to get sucked up that way!
I have bought a derelict house with a big derelict pond! It is pear shaped and about 14 meters long, being 6 meters at one end going down to 3 meters at the shallow end with a concrete base. It fills up with rain water and I believe it used to have a water source going into it but this seems to blocked off. The pond is situated beneath a large Monterey pine tree which would be okay if it wasn’t inhabited by rooks! So I am in the process of taking out years of sticks that have been dropped into the water which smells and is green!! There is also years of mud and detritous sitting on the bottom of the pond. I can’t do anything about the rooks but I can clean out the pond as we do get mallard ducks here. I have no desire to have fish. I thought I should invest in a pond vacuum? After I have removed the sicks etc. Any ideas??
Hi Virginia,
Congrats on the new house and pond!
Since you don’t want fish, simply performing a good bottom clean of the muck and a partial/full (50-100%) water change would be a good way to re-fresh the system – both of which can indeed be done with a pond vacuum. You’d want a vacuum with a decent discharge length and some good reach, as your pond sounds fairly deep. I personally recommend some models here, with both the PondoVac 4 or Power-Cyclone models being great choices for larger ponds. With these vacs you can clean the bottom muck and remove the stagnant water at the same time by positioning the discharge hose a way from the pond (i.e., down a drain, or as a fertilizer for plants) and letting it drain.
You don’t always need heavy equipment like vacuums for wildlife ponds as it’s not recommended to clean them regularly, but as it sounds like your pond has deteriorated into quite a poor (and smelly) state, I feel it would be the easiest and least messy method if you can afford the investment.
Once the pond is drained and free of most muck (you can leave a thin layer, as it’s great for insects, wildlife and plant growth), let it re-fill naturally if you’re not in a rush or top it up with mains tap water. In future, I’d recommend adding a good variety of plants to keep the water healthy and to help attract more wildlife to the pond. I’m including some articles below which may help by expanding some of these topics:
https://pondinformer.com/wildlife-pond-maintenance-guide/
https://pondinformer.com/how-to-attract-ducks-to-ponds/
https://pondinformer.com/best-pond-vacuum-cleaner/
https://pondinformer.com/category/pond-plants/
Do let me know if you have any more questions or would like further advice. Best of luck with the new pond!
I have been told that overfeeding goldfish can cause murky water, is this a fact. We have a small garden pond with a waterfall, which the birds love. We have many goldfish which breed prolifically (we keep the numbers down by giving some away every year). We would really love to have a clear pond so that we can see our fish. Please advise how we can achieve this. Marion.
Hi Marion,
Yes, overfeeding can indeed cause murky water, as well as other potential problems with water quality, such as high ammonia and nitrite levels. Also, if your goldfish are breeding constantly, they’ll be releasing a large amount of pheromones and organic proteins into the water, which are likely contributing to the poor water clarity alongside the food waste.
Have you performed a water quality test recently? If so, what are the results showing? It’s always important for us to first try to determine the root cause of the murkiness, as this will help us to prevent it occurring again in future.
If you’re interested, further reading on murky ponds here – https://pondinformer.com/how-to-clear-cloudy-pond-water/
We have just moved and have a pond in the garden, there are a number of fish in it but the water is so murky it is difficult to see how many, We have cleaned out the filters and replaced a faulty UV lamp and when we drain water of we get a green sludge even if we drain every four or five days, we are obviously not draining the whole pond just enough to get rid of the green sludge. The water does seem to be clearing so we feel we are getting there however we have now noticed two large sturgeon in there. We have been here 8 weeks and have only just started seeing these each evening, I believe we should be feeding them something other than Koi food so will be getting something in the next day or so. Is there something drastic we have done to make the sturgeon suddenly appear or is this a good thing?
Hi Glen,
Congrats on the new pond!
Sturgeon are bottom feeders and will spend most of their time swimming close to the pond floor, which probably explains why you may not have seen them until you drained most the water! Also, if you have some bottom muck or settled debris, the sturgeon will be constantly browsing through it and kicking it up into the water, contributing to the murkiness. Whether the murky water or sludge is actually an issue for the sturgeon will depend on your water quality parameters. The first thing I’d do in your situation is pickup a broad range water quality test kit and determine parameters for ammonia, nitrites, nitrates, pH and alkalinity (KH). If all look good, removing the sludge is a personal preference, but if you have plants and wildlife, you’d want to leave a bit so they have plenty of nutrients to root and continue to grow. If your ammonia is showing as high, removing the sludge may be beneficial, which can be done manually with a shovel/rake, or more easily with a pond vacuum. Depending on how large the pond is, and how many fish you have, weekly 10-30% water changes may also be ideal to keep waste compounds low and water clarity good.
Since the pond sounds very established, the sturgeon likely have some natural food available (insects etc.), but they’d also eat the koi feed as soon as it sinks and hits the pond floor. Purchasing a sinking sturgeon feed is obviously better long term (including some of my recommendations below!), but they should be fine with either a koi or goldfish feed for the time being.
Here are some articles which may help with the new pond, but if you have any specific questions, I’d be happy to help if I’m able!
https://pondinformer.com/pond-sturgeon-guide/
https://pondinformer.com/best-sturgeon-food/
https://pondinformer.com/best-pond-water-test-kit/
https://pondinformer.com/koi-pond-water-change-guide/
https://pondinformer.com/how-to-dechlorinate-pond-water/
https://pondinformer.com/best-pond-vacuum-cleaner/
very helpful
Hi Steve,
Thanks for the comment! Glad to hear the article was helpful to you.
Is there any point in adding “beneficial bacteria ” to break up pond sludge when you have a UV lamp installed?
Also, my pond has loose pebbles on the bottom, can a pond vacuum work in these conditions?
Thanks for all the help
Hi S.T.,
Your UV lamp shouldn’t interfere with beneficial bacteria, as these normally settle and establish on substrate and the UV light will only kill what’s within direct range of the light. This depends somewhat on the strength of your UV light, but overall it’s very unlikely that it will kill all bacteria, whether good or bad. You should be just fine!
As for the loose pebbles, I would recommending using a net or manual skimmer to get those out first so that you don’t risk damaging the vacuum.
We had our Koi pond professionally cleaned earlier this year. After reading your article and other materials, I believe I can do it myself. My question is similar to the previous one asked by S. T. Dupont. The entire bottom of our Koi pond is small rocks, larger than pebbles, but there is about two-three inches of pebbles on the bottom. The rocks do get covered with sludge/algae as well. How would I clean all the rocks? Is there a device that can suck up the rocks, clean them, and spit them back into the pond, or is there some big sieve that can be bought? It doesn’t seem like I’d be able to use a vacuum on the bottom of my pond.
Arleen,
There have been studies and successful experiments utilizing water hyacinth as an effective component in anaerobic waste treatment facilities. Our community’s sanitary sewer authority considered using them several years ago only to find winter water temps here in northern NJ are too chilly. I suggest this simply as a “hybrid” line of inquiry you might find worth pursuing.
Hi, I’ve got a medium sized pond, with no fish just natural wildlife. Frogs, newts and currently tadpoles.
Recently had a couple of ducks move in and the water has naturally become murky.
I love having the ducks but don’t want the water quality to drop and effect the other creatures.
I guess I will need to wait for the tadpoles to mature but is there anything in the meantime that can help, would a filter be able to cope with duck debris?
Thanks
Jen
Hi. We have a .25 acre pond that has a lot of silt on the bottom. We want to add some minnows, blue gill and bass. Not many, maybe a dozen blue gill and a half dozen bass and catfish. The water is clear and only a few feet deep. We live in northern Georgia. We plan on using aeration. Do we need to dig the pond out first? Will the fish survive in summer? There are trees and some vegetation around the sides. Thanks
I have to clean my filter pads twice a day and the leaf net In the intake box. The water was crystal clear when the string algae was in there but then when we start cleaning the string algae out with algae fix the water turns brown and mucky. We have to hose off the filters as they are full of muck twice a day. The bottom of the pond doesn’t really have “muck”. We don’t have a pond vacuum but will buy one if that’s what the problem is. Luck is growing on the slate of the waterfall and we scrape it off like thick pudding. All winter long the water is crystal clear. Please help
I live in a small retirement condo community (74 units). We have a storm retention pool (required for parking water runoff) that I have turned into a pond with fish, frogs, water lilies and water iris. I keep the bacterial levels healthy and use special fish to keep the algae down rather than using chemicals. Ducks and Geese fly in daily and I even have a Crane that swings by to eat minnows and small frogs.
The pool is silting in and I am looking for a way to remove the silt without draining the pool and not killing the animal life. The pool is about 100x40x4 feet and I have a water fountain (shoots water about 20+ feet high) for airing the pool and keep a current going.
Is there some way that I could pump out the mud over time? I do not have to do this all at once and I am not afraid to “wade in” and get muddy/dirty.
I am open to suggestions.
Hi I have been cleaning out my pond by net and vacum, water is very murky will this harm the fish. I have been clearing out the sludge over the past week in stages as water gets to cloudy.
The pond is 12ft by 5ft . I must have cleaned out 10 large buckets of sludge so far. I have some flamingo chippings and gold cast chippings are they safe for the pond and also some large rocks i got from garden center. Also shoiuld i leave some sludge. We do have frogs but i removed them as one grabbed a fish and wouldnt let go. There are newts in pond too.