| KFG,
In a mud pond (assuming no lime or anything of the sort), algae is the main culprit for pH swings. Algae, like all plants, release CO2 in the water during the night. CO2 dissolved in the water makes carbonic acid, which drags the pH down.
Algae in a mud pond is a good thing as it is contributing to the denitrification of the koi by-products. However, too much algae can cause problems as pH swings increase with algae contents. This is why in extreme cases, some kind of algae control is required in a mud pond.
It is not as simple as that of course :-) since if you remove algae, denitrification will be impaired. It is all a question of balance between fish load (ammonia) and algae, where the fish load does not require too much algae for denitrification, and so on (remove the fertilizer and the algae won't grow). Even this is simpler than what really happens butt gives you the idea about your question.
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Arthur
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