Well, for whatever good it may do, here's some questions:
What did you use to treat the flukes?
Is there treated lumber anywhere around the pond... decking, shade structure?
How does all that rainwater overflow to exit the pond, & where does it go?
Are there trees or anything overhanging the pond that drips into it with the rain?
Lots of rain often means lots of mosquitoes...Has there been mosquito spraying in the area? [We get lovely spray trucks drive through at 3am when mosquitoes become serious. Gov't budget crises this year may eliminate those.

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You may not have been doing anything different to the pond, but the rain would have other things being done differently... or neighbors doing something different.
Are you sure nothing has been done differently? ...not anything? How about something different, an improvement, or treatment for algae etc a month before you first notice anything?
Have you checked for stray voltage?
Describe your water change regimen.
Fading color on tosai would not cause me concern... stuff happens. It's the older ones that cause concern.