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Using potassium permanganate can and does kill fish.  Trust me, I have killed many fish in my early ponding years by not fully understanding just how Potassium Permanganate works.
It is very important that you read through the following and understand exactly what you are doing and why you are doing it.
a bigger filter regular water changes less fish
siphoning off the bottom or vacuuming at least every week or so.
Koi Video In this video I just added potassium permanganate to the upper pond

Koi Video   The first video is shaky because my camera was not working properly.  You are overlooking my lower pond which is 15,000 gallons.  Although the water is purple, it is not easily seen because it is cloudy and overcast outside and about 2 hours before dusk.

Koi Video  The second video is much better and from a different view.  And the camera is finally working better.  The view of the waterfall returning to the lower pond.  The middle pond returning to the two waterfall basins that lead to the lower pond.

Koi Video  The third video is our middle pond, a view of the bridge, the water returning from the streambed to the middle pond and then a view of the middle pond returning to the waterfalls and then the lower pond.  The middle pond has part of my lily collection.  We had to trim back the lilies because they were so massive that they were interfering with the water movement in the middle pond.

Koi Video  The fourth video is the waterfall from the upper pond to the streambed that leads to the middle pond.  From the upper pond you can see the skimmer from the middle pond returning from the middle pond skimmer.  Note all the plants growing in the streambed are soil-less!  The bare root plant was wedged between rocks in the streambed this past spring.  They are growing in just a few inches of water!

Koi Video  The fifth video shows a view of the upper pond returning to the streambed

Koi Video  The upper pond is actually the beginning of our pond.  This the view that one sees when they enter the back yard.  There is an arbor that we grow grapes on that is the entrance to the back yard.

The sixth video is the last for the night. 

Tomorrow I will add more to show the after effects of the PP and then how it looks after I have added 3 quarts of hydrogen peroxide

a bigger filter regular water changes less fish
siphoning off the bottom or vacuuming at least  every week or so.

If you follow these directions to the "letter" you will not have any problems. DO NOT INCREASE THE DOSAGE FOR ANY REASON!!

The following treatment will kill algae and dissolve organic matter (uneaten fish food, leaves, mulm etc). It is safe to use with pond plants and fish, so do not remove these from the pond

Plan to do this treatment while you can stay right by the pond the entire time. Should the fish start "gasping" at the surface, immediately add hydrogen peroxide. If you walk away and the fish get in trouble you may come back and find that they are all dead. I am very serious about this!! You MUST watch the fish at all times!!! The fish will begin to move close to the surface as the treatment progresses, and that is ok. They may occasionally come up to the surface for air, and that is ok too.

I am talking about all of the fish gasping hard at the surface. If this happens immediately add the hydrogen peroxide.

Add potassium permanganate at the rate of one TEAspoon per 1,000 gallons. MEASURE VERY CAREFULLY. Do not get this in your eyes, or on your skin. Stand down wind so there is no chance that you will breathe in the dust from it. Potassium Permanganate is a very strong oxidizer. I'll give you a couple of hints in addition here:
If you have any question about color, fill a white five gallon bucket of water with pond water and stare at it in full sunlight. Still can't tell if its pink? Add five drops of Hydrogen Peroxide (3%) There should be a *radical* color change. No color change? Then the water isn't really pink and you need to add more potassium permanganate. Ponds which have a high load of organics can eat-up a lot of potassium. Be warned. Your first couple of doses may only last a few minutes before they turn yellow or brown. Keep workring on it.
This is no joke. You need to have every possible bit of aeration happening and you want to keep it happening for at least 8 hours after the PP treatment is over. Potassium permanganate can drop the O2  (oxygen)content in a warm pond by quite a bit. We don't want this to happen when your fish is already oxygen-stressed.
Hydrogen Peroxide instantly terminates the effects of potassium permanganate in an emergency. If the fish start to crash, add hydrogen peroxide using 1 quart for 5000 gallons of water. Do not overdose with the peroxide!! Measure CAREFULLY. The treatment will grind to a halt in about 60 seconds (given good pond circulation). H2O2 instantly decolorizes the pond after treatment so you can check on the fish. It also adds a bit of oxygen to the water as well. If your fish starts to crash, remove him to a separate container and add 1 cc of hydrogen peroxide per gallon of water . He should rally in under an hour.
PP will sterilize your biofilter in about 10 minutes flat if you don't bypass it. The biofilter may experience a bit of a stumble in warm weather, but this isn't usually a problem. If you can rig a small pump or air stone inside your biofilter, this would be ideal.... but not critical. At this point the fish is the primary concern.

I'd like to see you accomplish the potassium permanganate treatment (above) TWICE over the course of a week. Ideally, you'll wait 2 days between doses.

This should happen over the course of 8 to 10 hours. The dead algae will drop to the bottom of the pond. You need to siphon this "stuff" off the bottom of the pond a sludge remover to the pond to help it break down of your pump is not big enough to remove it to your filter. If your pump and filter is big enough to remove the dead organics, make sure you clean your filter every few hours

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