You can't go wrong with knowing the water quality of the pond and the source, so that's certainly a good suggestion. I would not forget about the crawdads, however.

When I bought my place it had a silted in 100 x 170 foot pond that was only 2 foot deep...no vegetation what's so ever. Long story short, it turned out to have a lot of crawdads in it and no fish to act as predator. Take a crawdad trap (or even a long handled dip net with finer mesh) and sample the pond. My old pond would produce 20 to 30 crawdads in an hour or two using a wire trap and some dry dog food. The crawdads were northern virile species and were typically 1 to 3 inches long. Side note: I threw some creek fish in the pond "for fun" and within a couple years the crawdad trap couldn't catch more than a few and the plant life started to return (mostly FA). The creek fish turned out to be GSF and there was a thousand or so when we drained the pond for renovation.

Do you have access to any creek fish? you could catch any ole' pan fish and plop it in a 5 gallon bucket full of the pond water with an air stone and see if it lives for a few days. Keep it in a cool, place like a basement with a cover and see if makes it. Kind of a canary test.

I can not really blame an overpopulation of crawdads on the death of the fish really. And I would not be able to suggest why crawdads would survive bad water over the Koi. Were the Koi fed or did they rely on the vegetation?

Fish on!,
Noel