Why Is My Pond Water Black? (And How to Fix it)


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Why is my Pond Water Black? Guide to Clearing Black Water Problems (updated)

black pond water
Pond water can simply look black due to surface reflection, but can also be caused by a build-up of waste and bad bacteria.

Speaking from experience, it can be quite a difficult task to keep a garden pond clear all year round, especially in months such as Autumn where there is a large amount of debris settling in the water. Pond water will naturally shift in color throughout the year; becoming more “yellow” in autumn as tannin (organic color) leaks from fallen leaves, and more “green” in summer as algae tries to bloom under the sunlight. In most cases this is a harmless seasonal change that will balance out with regular pond maintenance, good filtration, and stable water conditions. Although this rapid change in color can see scary, in most cases there is little you can do but let the eco-system catch up and do it’s work!

However, even though seasonal changes in color can be natural and nothing to worry about, if you notice your water is shifting to a much darker “black” color, it’s probably time to investigate further. A black color in the pond, whether it’s in the water or on the pond liner, is often a warning sign of a growing imbalance that needs attention. It’s rare for this type of color to occur rapidly, and it is more commonly the result of an long term problem, such as a lack of aeration causing beneficial bacteria to die and sludge to increase. In most cases of rapid black color, the cause can be attributed to treatments, medicines, chemicals, and even water dyes. Basically, something man-made is getting into the pond and the pond is not happy about it!

Whatever the reason, a black pond is not a good sign and needs to be investigated and treated before the problem can cause permanent damage to fish and the eco-system. Below in this article we cover the best treatment steps for black water, and provide more information on its causes and the potential risk factors.

What causes black pond water to occur? 

1) Excess Waste & Low Oxygen Conditions (Most Common)

why is my pond water black
Black pond water is most often caused by a lack of aeration, poor filtration, and a build-up of waste.

The most common cause of black pond water is due to build up of waste, a lack of aeration, and the growth of slow-digesting anaerobic bacteria. Although cleaning out muck in your pond can seem like an unnecessary chore, unless you have a strong filtration system and plenty of aeration in place, beneficial bacteria can’t always keep up with demands. To breakdown all the debris, sludge, and gunk in the pond, beneficial bacteria require lots and lots of dissolved oxygen to function efficiently. This type of bacteria, the “good bacteria”, is aerobic in nature; meaning it utilizes oxygen (O2) for energy.

In seasons with heavy debris fall, such as autumn, or if you simply don’t clean out excess waste regularly, oxygen content will slowly drop and beneficial bacteria will die off. At this point your pond may look brown in color due to the leaking tannin (color) from decaying debris, but will eventually turn black as the muck becomes filled with anaerobic bacteria which slowly break down waste and release potent waste products. This kind of bacteria (the “bad” kind) functions in low oxygen conditions, thriving in the rotting humas which turns dark in appearance as things decay on the pond floor. This cause is often easy to spot as the black color is mostly on the pond liner as thick sludge, with an accompanying smell of sewage and rotten eggs around the water.

2) Leaks or Damage to Pond Liner 

Another common cause of black pond is damage or leaks to the pond liner which cause sediment and minerals to leech into water. In most cases this problem would bring about a brown or yellow color, but this can also turn black as sediment levels build. If you’re in an area with high levels of mineral content in the soil, especially manganese, this could also be causing the darker shade of water color.

3) Water Dyes, Medicines, or Chemical Treatments

Rapid changes in black color can be attributed to chemical imbalances, often from water treatments, medicines, or water dyes. Although many natural water dyes have a active life-span before they disappear, residue can linger for months afterwards causing a dark appearance and increased surface reflection.

4) Black Algae or Fungus Growth

A final possible cause, although a very rare one in ponds, is the growth of black algae (cyanobacteria) or rare types of fungus. This is potentially the most damaging cause of black pond water, but assuming your pond is in mostly good condition, it’s unlikely to be the case. If you suspect you have black algae growth, it can be removed with similar treatments as regular green algae with good results.

Is black water dangerous to koi and goldfish?

black water poor water quality
Depending on the cause, black water could be an immediate threat or early warning sign of growing problems.

The color (tannin) which often causes water to change appearance may not be directly dangerous to pond fish, but the underlying cause most certainly can be! Both goldfish and koi thrive in stable water conditions and can quickly suffer if water quality declines. Ponds with fish should be well aerated, have good water filtration, and be properly maintained and cleaned to stop waste building over the year. As the most common cause of black water is low quality conditions causing bacteria to die off, oxygen to decrease, and sludge to increase, it’s a problem that can seriously harm or even kill pond fish if left untreated.

Overuse of chemical treatments, medicines, and even water dyes can also place stress on pond fish even if the ingredients are mostly “natural” in nature. Many will leave residue in the pond long after they have been used, and this can cause gradual problems with water quality over time.

Although rare, black algae is not immediately harmful to fish but can be incredibly stubborn and tough to remove once it’s settled in the pond. Unlike green algae which quickly booms and dies in summer months, black algae is a slow grower, and problems usually occur after a long period of time after its been able to spread. If you notice any black algae on the pond liner sides, it’s best to quickly scrub it off before it can become a more permanent feature.


Best Black Pond Water Treatment & Preventive Methods (Step-by-Step Guide)

Before starting: Always test water quality throughout the year, especially before and after performing a clean or treatment. This ensures you’re aware of any potential problems and you’re treating the correct cause (i.e, cleaning to reduce excess ammonia). Check here for our guide on testing water quality in ponds!

Step 1: Reduce Excess Waste & Bottom Muck

Sludge can easily be cleaned with nets or vacuums, with vacs being especially useful in larger ponds.

If you notice your black water problems have come about gradually, and the black is mainly on the sides and floor of the pond, your issue is almost certainly related to excess waste. As mentioned above, if your biological filtration becomes overloaded with waste, eventually beneficial bacteria will die, and bad (smelly) bacteria will rise – leading to a lot of black gunk.

The best way to resolve this issue is by performing a deep clean of the pond liner using an electric water vacuum or wide-brim pond net. Although you may have read elsewhere that adding more beneficial bacteria will help reduce the muck, this actually may lead to even more muck and even greater problems with water quality! Beneficial bacteria require lots of dissolved oxygen to function, and simply adding them to a low-oxygenated environment with large amounts of waste will cause them to die off and further increase waste levels. If your pond has gotten to the stage where you’re experiencing black water, the conditions are probably no longer suitable for beneficial bacteria to colonize.

So, first things first, time to clean out the muck with a vacuum or net, with the vac being much more effective for larger ponds or ponds with fish. You should aim to remove about 90% of sludge from the pond floor, leaving a small amount behind so good beneficial bacteria have something to eat when they’re able to start colonizing again. If you’re dealing with black sludge, it’ll have a high level of hydrogen sulfide produced from the slow-digesting bacteria, so a strong smell of rotten eggs is normal and just something to bare while cleaning!


Step 2: Improve Filtration & Water Quality

water quality test kit
Pond water should be tested throughout the year to ensure good water quality is maintained.

After performing a clean out of any excess waste, it’s time to take a look at water quality and your water filtration. If you haven’t already, you should perform a water test to determine the current parameters and the quality of your water.

If your black water problems were caused by a build up of sludge and anaerobic bacteria, your water quality will likely still be very poor even after a clean out. At this point you’ll want to inspect your pond filter system, ensuring it is clean and free of debris, and consider adding extra beneficial bacteria to kick-start the new population. With a pond free of waste, oxygen levels will slowly start to increase and beneficial bacteria can gradually begin to re-colonize the pond and filter media. As they start to work again, ammonia and nitrite levels will also begin to fall as the bacteria start breaking down the substances into less harmful components, such as nitrates – a fertilizer for plants.

To help your biological filtration along, you can look at optimizing your filter media to maximize bacteria colonization, and you should also make sure to keep on top of proper maintenance so filters can perform their job optimally. Contrary to popular belief, even biological media needs to be cleaned sometimes, especially if it is covered in black gunk. If there is no oxygen in contact with the surface of the bio-media, no beneficial bacteria can function anyway, and they’ll be replaced with the slow-digesting bacteria you need to avoid.


Step 3: Increase Aeration & Oxygen Content

air pumps prevent black pond water
Dedicated air pumps can provide large amounts of oxygen direct to pond water all year round.

Low oxygen conditions not only decrease the efficiency of your biological filtration (beneficial bacteria), but will also place a large amount of stress on pond fish as they struggle to breath. Since both bacteria and fish benefit from large amounts of oxygen content, it is always a good idea to maintain a constant source of aeration year-round to keep everything ticking over!

Waterfalls, fountains, and even the natural flow from your filter outlet can provide plenty of aeration to ponds with low fish stocks or small fish. If you have a smaller garden pond,  but don’t want to spend money powering a electrical pump, you could even consider adding a solar power pump or aerator which will provide extra aeration to your waters with no recurring costs.

For larger ponds, or heavy stocked koi ponds, we recommend investing in a dedicated oxygenator system which will supply a constant stream of oxygen to waters all year. This is particularly important in both summer and winter where oxygen content is lower due to heat and top ice, but can be run constantly throughout the year for best results. Oxygenating the pond ensures that fish always have a surplus of dissolved O2 to breath, and also makes sure beneficial bacteria are functioning optimally and removing harmful waste substances efficiently. Preventing black muck is easier than fixing it after it has occurred, and making sure you have plenty of aeration and oxygen is a major piece of the puzzle!


Step 4: Inspect Pond Liner for Damage/Leaks

pond liner repair kit
Pond liner repair kits are an easy and quick way to patch up small leaks and tears in liner material.

If your issue is not related to black sludge, or you’ve tried the above steps and you still have black water, you should inspect the pond liner for damage. If you live in an area with a high amount of mineral content in the soil, even a small tear can leak sediment which can gradually stain water with color.

Pond liner damage is not always easy to find, especially in large or deep ponds which are stocked with fish. One method is to turn off all pond equipment temporarily and check the surface for small air bubbles which can give you a rough idea of the leaks location. Another method, although not so easy, is to drain the pond of water and inspect the sides for damage manually. Finally, a nice little DIY method which we have personally used is to place a small cup (egg cup sized) of milk into the pond and watching to see where the milk spreads. If there is a leak or damage, the milk will be pulled in that direction and you should be able to see this clearly with the white color showing the way.

Leaks may also be happening around the embankments of the pond, usually when the pond liner falls below the water line or from under equipment – such as skimmer boxes. This is easier to spot in comparison to a leak under the water as the liner will look folded and bunched compared to the surrounding material. In either case, be sure to check here for our full guide on leaky pond liners and what you can do to repair them.


Step 6: Remove Algae & Treat for Fungus

Natural algae treatments, such as Nualgi Ponds, can be effective in treating black, green, and string algae.

Although black algae is rare in ponds, if you find any spots appearing on the pond liner you should quickly scrub them off using a sterile brush or sponge. Normal algae treatments, such as UV clarifiers, can only deal with free-swimming green algae and won’t be able to combat algae attached to the pond liner. Even though you can combat these more stubborn algae spots with chemical treatments, we feel chemical treatments should only be used as a last resort, and we never recommend them if you have fish due to the high risk of fish death. If water quality is stable, black algae spots can be scrubbed away and a natural algae treatment, such as nualgi ponds, can be added to prevent it coming back.

Even though regular nuisance algae won’t cause black water directly, it will gradually contribute to waste as it blooms and dies off – eventually leading to muck and possible black sludge. If you have a large amount of algae, we recommend treating it before it can become a problem in future as it’s easier to control in the early stages.

In terms of fungus, this is even rarer than black algae as a cause of black water, but if you notice your fish are acting strange or showing signs of skin/fin rot, you can treat the pond with an anti-fungal and anti-parasite treatment to be on the safe side. Often fungal problems will resolve naturally as good water quality returns, but fish may need a helping hand if they’re already sick.


Step 7: Supplement with Activated Carbon (Remove Tannin)

activated carbon for ponds
Activated carbon treatments are useful for removing tannin, but won’t solve the root-cause.

An effective way to remove the color (tannin) causing the black water is with activated carbon treatments, but this should not be used as the only treatment unless the cause is related to pond dyes. Activated carbon will neutralize organic color and pollutants which leech from decaying debris, but can’t resolve the actual root-cause of the issue so the tannin will eventually come back. After the cause of the black water is resolved, you can then add activated carbon to your filter box to help remove lingering tannin and any residue left over from treatments.  If you know that the black water is being caused by a pond dye, you can simply use carbon to reduce the intensity of the color and neutralize any remaining residue.

Activated carbon is a great way to add a third stage of water filtration to ponds, and is especially effective for koi keepers wanting to maintain a high water quality standard year round. For more information on activated carbon treatments and how to use them, check our full guide on this here!

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