I have a 4 year old 12,000 gallon koi pond with a large waterfall. I went to clean the waterfall filters and add barley hay for the algae last weekend only to find thousands, maybe millions, of black fly larvae. I scraped the waterfall as best I could and turned the waterfall back on. The koi enjoyed a meal but when I turned off the waterfall the next day, several of them had been sucked back through the main filter/pump and adhered themselves to the waterfall again. Just now, I scraped again, then ran the waterfall for only a short time so they would fall back into the pond but turned off the pump so the koi could completely devour them.
I've placed wire around the pond to keep out critters and heron, and had to place netting over the pond because the osprey started swooping down. But black flies are an unexpected battle and not something I've read about in any pond books. I've never seen such horror... the waterfall was covered in what look like tiny leaches and egg-like structures attached to the rock. I recently purchased water plants... did they hitchhike? How can I get rid of them completely without harming my koi? I am unable to find any information online. Hoping for guidance or at least reassurance that my property will not be a source of the sky going dark with giant swarms of black flies and my poor dog being devoured by flies when I let him out.
Well, the good news is they are an indicator of good water quality and are a great food for your koi. The down-side is that control is pretty limited aside from physical removal as you have done. There are products containing Bacillus thuringiensis var. israelensis that are used for aquatic fly control. I would suggest asking a local pond supply store for fly control products that are safe for koi ponds.