Troubleshooting Unusual Pond Koi and Water Quality Problems

Published on October 29, 2021

crowded pond fish
A crowded pond has a higher likelihood of disease transmission.

We recently received a call from a customer who reported something they had not seen in more than 46 years. Their pond had been rebuilt last season, and the rebalancing act had become a bit of a mess, thanks in part to this season’s extremely hot weather. After getting the water quality in check, they noticed black spots the size of an eraser head starting to appear on their koi. They tried Googling “black spots,” but they hadn’t found the answer they were looking for.

We get calls like this all the time. Here is a collection of some unusual issues that could be observed in a pond.

Changes in Koi Color

Having hard water can cause the development of black “freckles” known as shimi, which were the “black spots” our customer was talking about. They mainly develop inside a Kohaku’s beni (red color), and they tend to have no effect on Kujaku, other metallic koi or the artistic Kikokuryu varieties.

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Black spots are not an illness, but if the customer were to see gray or greenish spots, I might become very worried. From my experience, black spots are either shimi or the result of a fish changing color.

Pond owners often buy a “perfect,” beautiful koi, only to watch the same fish lose all its color. This can be due to illness or simply because koi colors are genetic. If they had bought a noted Japanese koi for a high price with a guarantee of a good bloodline, there is a good chance that the koi would retain its color for many years.

However, water quality can have an influence on the colors of your fish. On a Showa, the black becomes the dominant and deciding color that makes or breaks it, as far as show-quality appearance goes. However, that black will probably take five to 10 years to emerge and take its place on the fish. The problem with black is that it tends to come and go. If it looks beautiful when you buy the fish, it will likely disappear by the time the fish is a few years older.

Carp Pox

Shimi (black spot)

Carp pox is a herpes simplex virus (Cyprinid herpesvirus 1). It raises blisters on the body of your fish during the colder months, but it should subside during warmer months. Of the koi and goldfish herpesviruses, carp pox is most like chicken pox in humans.
The virus is globally distributed in koi and common carp. Like any infectious disease, it is easily spread. And like herpesviruses in almost all other species, latent carriers can be present without ever showing any clinical signs. By the time you see clinical signs of carp pox on one fish, all the other fish likely already will have been infected.

It is rare that most fish show clinical signs of carp pox unless their immune system is not functioning well. While generally not life threatening, in severe cases, the viral infection also diminishes the fish’s immunity and leaves the lesion-filled (papilloma) area prone to a secondary infection by bacteria. It is not attractive, just like the cold sores that humans get, and any success you have with making it go away is probably coincidental. There is no proven treatment for a carp pox infection.

While it might make the fish look more pleasant, surgical removal of the lesions will not cure it of the virus. It will generally return the following year if conditions are right. A crowded pond has a higher likelihood of transmission because it is transmitted by body contact. Sooner or later, it will appear in everybody’s pond.

The only way to prevent the viral infection from spreading is to single out and destroy the infected fish and its environment. In my experience with carp pox, I have seen it on both koi and goldfish. I have told people to leave the fish alone and stop spending money treating something that can’t be cured. Euthanizing all the fish and sanitizing the pond is not a sure-fire cure, and it is not recommended.

Bleeding Fins

From the looks of this fish, there is something wrong with the water quality.

In my experience, capillary bleeding in fins or tails is not always restricted to the longfin koi exclusively. They seem to show this sign of stress sooner than standard koi — as soon as it reacts to something unsatisfactory in the pond water.

At first sight of this condition, perform water testing. See if there is any ammonia, nitrites or other levels that have changed recently. Has anyone sprayed trees near your yard? Increased aeration, a partial water change or shade over the pond during the summer could satisfy the koi.

Sometimes it means that the filter needs to be cleaned, or the pond needs to be vacuumed. It still could be a result of parasites, but it’s worthwhile to find out before you start using chemicals, which could make a small problem much worse. Find the source of the fish’s discomfort before you do anything. I’ve always been told not to treat if only one or two fish are showing symptoms. However, if all the fish are displaying signs of something, then they definitely need help.


While all koi can jump very well and very high, some are indeed jumpers by nature.

But then there are other reasons why normal, happy fish might jump out of the pond. If you are altering the pH — especially bringing it down — they may be more prone to jump out. Koi are fine with the pH going up, but they hate it when it suddenly drops.

Always follow directions closely when using chemicals in the pond. Even then, make changes very slowly if you must. If you have one of those jumping koi, look at your pond construction. That particular fish might benefit from improved surroundings, like rocks and plants to make it look to the fish like it cannot simply jump to another part of the pond. This tactic could keep him there where he belongs.

Red filter worms.

Red Worms

Many people are disgusted by these simple Aquatic Midge larvae that can show up in the pond filter. Having no idea what they are, their biggest fear is that they will be harmful to fish.

Little do these people know, we used to buy and feed these same worms to our aquarium fish. They were called tubifex worms or bloodworms in the trade. These are actually a sign that the pond is happy and healthy.

However, if you cannot stand cleaning your filter with “them” in there, you can easily remove them with Biological Mosquito Control (BMC). Aquatic Midge is on the list of larvae that are controlled by BMC, along with the larvae of black flies, mosquitoes and fungus gnats. Controlling them in this way will not harm your healthy ecology or your fish.

You could even drop the filter pads into the pond to let your koi have a nice live meal of worms!


Leeches could be a gift from wild birds visiting the pond.

Ugh! Sometimes we really do find leeches in the pond or in the filter. They should not attack your fish, but it depends on the type of leech, of course. They will be vectored by visiting birds and their poop.

This is the more gruesome side of owning a pond. (It also means your pond is not as clean as you might have thought.) When it happened to me, I had shaped the pond like a toilet bowl, with a bottom drain, excellent filtration and most of the bells and whistles. However, I also had a stream and three planted bogs attached to it. It attracted all kinds of wildlife, and something introduced leeches to the pond.

My answer was to hit it with potassium permanganate to clean up everything. Fish will eat the leeches if they have access to them. Salt will also kill leeches, so I may have been overreacting with the potassium permanganate. There are also other ways to trap and remove leeches.

A Crooked Koi

Oh, look! A crooked koi!

If a crooked-looking fish was not crooked when you bought it, you can rule out genetics or a birth defect. A broken back or other physical injury could be caused by an electrical storm, lightning hitting the pond or an electric short from a pump installed without a working ground fault circuit interrupter. These devices are not infallible, and even though they may be installed, they do fail from time to time.

No, you will not be able to cure it with medication; however, if the issue is related to nutritional scoliosis, it could be improved with vitamin C. Surgery is also an option when appropriate.



If your fish has an ulcer, that means an opening in the protective outer slime coat layer has been caused by either a parasite or an accident in the pond. Once this happens, invasive bacteria such as Aeromonas and Fusarium can enter the opening and rapidly take advantage of the opportunity. Many Fusarium deaths have been mistakenly attributed to Aeromonas.

The problem is often made worse when an ulcer starts on the underside of the fish, where you will not notice it until it is full blown. Even lost scales present an opportunity for bacteria to enter. When you have a fish with an ulcer, it is important to regulate osmotic balance for it to be able to focus its strength on healing. We use 0.3% to 0.6% salinity to balance the outside pressure with the internal pressure so that the fish does not have to expend its energy bailing out water. The fish can also be quarantined if you are able to catch him.

If you have plants in the pond, you will want to remove them or use 0.1% salinity. Sabbactisun herbal treatment is excellent in preventing secondary infection and promoting the healing process for ulcers.

Sudden Fish Deaths

These can be frustrating and are generally blamed on the last thing added to the pond. One thing we would never think of is the day we added a particular fish to the pond. It’s true — the way we add new fish to a pond has a lot to do with how the fish fare later on.

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If a fish has been bagged for several hours or days before being introduced, the first thing to do is float the bag on the surface to acclimate the temperature for about 20 to 30 minutes. Then, open the bag, immediately remove the fish and put it into the pond. Throw away the bag water outside the pond. If you add any pond water to the bag, you will have inadvertently killed your fish by creating toxic ammonia in the bag.

Another problem is in doing water changes. When you draw the water down, add the amount of Dechlorinator before you begin to refill the pond with new water. I hear frightful stories of people adding Dechlorinator after they have refilled the pond. By that time, you have already burned their gills. If you do this often enough, the fish will have permanently impaired gills. Sooner or later, this could kill them.

Another thing to remember is that carp reportedly have the lowest threshold to copper. Copper is a toxic heavy metal and a bio-accumulative that, like mercury, can kill in small amounts. In koi, it is stored in the muscular tissues, heart, lungs or brain until it reaches a level of toxicity that causes it to die a “healthy death.”

Strange Fish Poop

We saved the best for last! Have you ever received a help call from a customer because their fish has a long white or black “worm” coming out of it? This is a big emergency! I wonder how many ponds this has happened to and the owner did not call.
Fish beware! No pooping allowed here!

Aqua UV

2 thoughts on “Troubleshooting Unusual Pond Koi and Water Quality Problems”

  1. My KOI are older and larger than last year… but today they are gone! There is a new family of fox’s in the neighborhood. I have netting over the pond because of the hawks. Medium size stones hold down the fiber poles that support the net. 350 gallons 5 Koe. Poked around with a clean stick. Why would they be staying on the bottom? Would thunder and lightning make them hide?

    1. When I’ve had a visit from the Heron or a fox my Koi and other fish all stay on the bottom for a few days, they’ve been spooked, my pond is well netted and I have a camera over it so i can see who visited, no fish get taken but it still appts them for a while. Sometimes when I e had a really bad Thunder storm my fish will go to the bottom or if the pressures really high they go by the filter for more oxygen, the Thundery air pressure can take oxygen of of the water, but they’re usually ok after the Thunders passed. I’d put it down to visitors spooking them.

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