When it comes the time to change the water in any fish enviroment it would not be a good idea to change all of the water at the same time. Any sudden enviroment changes are not a welcome thing by fish at all. This can be considered the same as lakes to most people. Any change such as temperature, pH, or chemistry to the water.
If you have a good filtration system it should have a biological filter and also a mechanical filter. The filter that removes the fish waste that is dissolved is the biological filter. This shouldn’t be confused with puddles in any circumstances. The filter will turn the waste into nitrite and then into nitrate. This happen to be done all in the filter system. Nitrate is a chemical that is harmless to the fish but it will let build up produce in your pond that may harm your fish.
Some water plants can be bought to help in the removal of nitrates. It will take a lot of plants to take out any amount of nitrates that you would need them to. Some people use a trickle tower to remove any nitrates in their koi pond but they are not that cheap and by giving your water a partial change is much more cost efficient.
You should do a water change often but it only needs to be about ten percent maybe every couple weeks. When you do your water changes you should also check for nitrate levels this will prevent any discoloration in your koi pond. You can test for nitrate using a test kit that will let you measure the nitrate level, pH, nitrite, and oxygen level in your koi pond.
If you are going to use tap water to replace any water in your koi pond it is a good idea to use additives to remove the chlorine that is added to the water. Chlorine will come out of the water if it sits for a few hours also.