One of my koi, was healthy, swimming around and eating on Tuesday afternoon at about 2:15 pm; at 2:40 pm he was found floating upside down at the side of the pond (1000 gallon pond with 3 koi and 2 goldfish) practically lifeless. We placed him in a separate tub of water with a bubbler for the rest of the afternoon. That night at about 9:00 pm he had righted himself and was slowly swimming around in the tub, so we returned him to the pond. What might have caused this situation?
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Without more detailed information, it is difficult to speculate, but there are certain "hints" in your question that suggests it might be due to low oxygen levels. First it occurred mid-afternoon, typically the warmest time of the day. Warm water loses its capacity to hold onto oxygen, particularly at temperatures above 85 degrees Fahrenheit. Warm water combined with poor water circulation can create pockets of oxygen-depleted water harmful to pond inhabitants.
Your koi's positive reaction to enhanced aeration during the cool of the night when water is capable of holding onto more oxygen, is another "hint." If you are experiencing an exceptionally warm summer in your area, it might be a good idea to enhance water movement and aeration in your pond. Improved circulation helps eliminate stratification or development of harmful, oxygen poor layers.
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