Frequently Asked Questions

Unexplained fish mortalities


I have placed this subject under Frequently asked questions because of the many varied call-outs that I must attend to when either one fish dies unexpectedly, or I am called to a pond that is in a sorry state where a large contingent of the fish are belly up.

This is something that most koi keepers will experience one time or the other in this fascinating hobby. It may be the sudden death of one koi in the collection, or it may be mass mortalities. This is not a pleasant subject, nor is it a pleasant task, but one will have to investigate the possible causes to protect the collection. On the other hand if there are no sure answers, at least one will be able to eliminate some possibilities as the cause of this phenomenon.

The riddle of sudden deaths in a pond is not very difficult to solve. The most difficult case is the sudden death of a single fish while there is no apparent change in behaviour or other symptoms in any of the fish in the collection. For obvious reasons one will have a different approach when a single fish die than when there are mass mortalities in the pond. The most sensible and practical way of trying to find answers is to approach the investigation systematically.

The first step is to determine the overall “first glance” health situation of the rest of the collection. Are the rest of the koi exhibiting abnormal behaviour or are they swimming normally? If there are others that are keeping on their own it may be the start of some problem that may affect all the koi. Are there any fish in the collection flashing, excreting excess mucus, clamped fins, hanging near water returns etc? If there is any indication that something is wrong with other fish in the pond the problem is not contained to the single dead fish. In such a case it will be better to concentrate on the pond, the system and the koi collection itself. If there are no sign of disease in the collection, it will be prudent to regard this as a “single fish death” and the investigation can then concentrate on the following step.

Single fish death

When a single fish is found dead in a pond, it normally comes as a shock with no pre-warning signs. Most of the time the owner is totally baffled and armed with the minimum information, will commence phoning around asking all kind of questions to fellow koi keepers who will not have the faintest idea what happened. These koi friends will however, as a courtesy offer their theories and confuse the issue further.

The best way to go about the quest to find answers is to start immediately. The dead fish can be placed in the refrigerator, but do not postpone the autopsy for more than an hour or two. If you have placed the fish in the freezer, forget about finding answers. It is a promise, by the time the fish the fish has thawed, even the most experienced person will struggle to read the clinical signs to try and determine the cause of death.

Carry out a visual inspection, looking for obvious signs that may have caused the death of the fish. Signs to look for are obvious external damage, ulcers in the mouth or underneath the fish, swelling or redness of abdominal area, and damaged gill filaments. You can only determine if there is damage at this stage, because the gills of a dead fish may be discoloured and will not give enough clues to accurately determine any abnormality. If you know your fish, look for muscle/weight loss, firmness of muscle tissue, sunken eyes, cloudy eyes, bulging eyes, even cuticle, unusual head to body proportion, or symmetric body outline when viewed from the dorsal area. If the fish is not symmetrical, it may indicate a tumour or an injured spinal column.

If there are no obvious reasons for the fish’s death or abnormalities in appearance, it may be necessary to do a fairly simple autopsy. To do an autopsy, it is necessary to have a basic understanding of koi anatomy. Koi anatomy can be viewed here.

Start by removing the gill covers and then cut one branchial arch at the top and the bottom. Remove the arch and study it under a microscope at 10x. Zoom in on the filament. The filament should resemble a fern with small hair like “leaves”. Deformed, damaged filament and lamellae will easily be noticed, because it will resemble solid “twigs”.

  operc_removed gill
  Removed gill Cover                                                                                     Dammaged Gills

For the hobbyist it will not be possible to do a detailed autopsy, but if the intention is to send various samples for analysis, the outside of the fish as well as the instruments should be sterilised with surgical spirit to prevent contamination of the samples. Place the fish on a non-slip surface.

Use a strong pair of scissors and make the following incisions.

Photo: Johan Jacobs

Remove the wall of the coelomic cavity and determine if there are abnormal adhesions of organs to it. Most of the internal organs should now be exposed Also look at the inside of this cavity wall for any obvious red or pinkness that may point to an infection.

Drawing: Amelia Odendaal

Examine a sample of the faeces under the microscope for worm eggs or Heximita. The swim bladder should be firm and white/silver in colour. Pink or red appearance shows infection. Dissect the swim bladder and determine if there are any liquid or fungus-like growths inside. Next one can concentrate on the other vital organs like the kidney, spleen, liver and heart. Determine if there are any obvious abnormalities or haemorrhage.  If you wish to take samples for analysis it is now the time to remove the needed samples and place them in sterilised sealed containers.

During such a basic autopsy it is fairly simple to determine the cause of death if it was caused by a tumour.


Systemic bacterial infection,


Or when the fish became egg-bound


Photo: Johan Jacobs


The challenge with accurately trying to determine the cause of death of a koi is that many health problems are inherited and it is not necessary caused by a disease-causing organism. In other words, there is nothing visual or diagnosable to determine the cause of death. In such a case it is better to accept the death and move on.

In a case where the cause of death could not be established by a simple autopsy, it would be advisable to take a mucus scrape from one of the “healthy” fish in the collection and also to take a number of key water tests to be absolutely sure that the death could be regarded as a “single fish death”.

Mass mortalities

When you notice more than one dead fish and the rest of the collection are displaying abnormal behaviour, then the quest to determine the cause of this occurrence should start with a number of key water tests. Mass mortalities are mostly caused by environmental problems, while mortalities over an extended period can be attributable to disease.


The best option is to start with water tests.

The ideal readings should be the following, although small deviations should not lead to mass mortalities, merely unhappy fish.

Ammonia – less than 0, 1 ppm
Nitrites – less than 0, 2 ppm
Nitrates – less than 50 ppm
pH – 7 to 8
Oxygen – more than 5 ppm
Alkalinity – 50 to 150 ppm
Hardness – 70 to 150 ppm
Salinity – up to 0, 3%
Chlorine – less than 0, 05 ppm

If the readings differ substantially from the above, a large water change should be effected as soon as possible, to get the fish out of danger, but the root cause of the deviation should be determined because such a deviation points to a problem in the filter system.

If the readings do not differ substantially it is still worthwhile to go through the system systematically, to ensure that there are no sludge build-up in the filter material or filter sump, or especially in the sand filter that may have caused methane gas to be released into the water.

Consider new or blooming poisonous plants in the vicinity of pond? The internet is a valuable source where one can determine what plants are poisonous and what not.

The next step is to put a hand into the pond to see if small bubbles form on the skin. If that is the case, inspect the dead fish for small air bubbles in the fins or around the eyes. Such bubbles can indicate gas bubble disease and the problem can possibly be a small leak between the pond and the pump or the pond level has dropped sufficiently for the pump to suck air.

The final course of action is to retrace the last couple of weeks or so to try to identify whether you have done anything differently with the pond, water, koi or on the property.

I have encountered most of the under mentioned and any one of them or a combination could have caused a problem in the pond. Consider each one carefully and discard the obvious things that could not have had an influence.

Recent medication added to the pond. Overdose or medication was old and turned toxic? Maybe some witchdoctor/snake oil advice on medication by a friend?

Recent water changes could be the problem. Activated Carbon reaches a saturation point quicker than most people think. Did you ad de-chlorinator? Did you forget the hosepipe in the pond? Did the water authority increased the chlorine dosage or changed to Chloramine?

Was the filter media disturbed recently, causing possible toxins to flow into the pond?

Did you have the roof or guttering painted and the contractor spill paint into the pond?

Recent rains and you have just added a pergola constructed out of unsealed treated timber. Maybe runoff water from the garden?

Did someone do maintenance on the house or buildings nearby? Perhaps toxins entered the pond?

Did children have unsupervised access to the pond? I know of a case where such children dumped a bag of compost into the pond.

Appliance malfunction, a tripped breaker or thunderstorm preceding the sudden death may have caused electrocution?

Did the pest control company perform any task on the property?

Did you leave an open paint can or paint remover next to the air pump?

Did you change your water source recently? Perhaps from tap water to borehole and heavy metal poisoning took place?

If you have eliminated all the above and maybe more, the last step is to investigate the possibility of possible pathogens. A mucus scrape and a small gill biopsy can be done and inspected under the microscope. Sometimes Costia are very difficult to see, but if there are mass mortalities the sample should be crawling with parasites.

By this time it is hoped that the cause of the mass mortalities has been established. If not, the alternatives are a bacterial culture by a laboratory of some of the organs obtained exactly as described under a single fish death and the submission of a gill swab for KHV testing.

Last Updated on Saturday, 30 October 2010 09:50