I'd have a hard time believing that pesticides/herbicides were the culprit if you haven't had a die off of other aquatic species. The addition of chemicals would adversely affect O2, and the fish would be the first to go. I would also think that a pesticide or herbicide would dilute to the point where a lethal dose wouldn't be possible for reptiles unless you had a very concentrated source within your runoff basin.
Is it possible that it's a viral or bacterial infection introduced from an upstream source that your turtles don't have a natural immunity to? Or possibly a new parasite or fungus? All of these things can cause die-offs within small communities.
I know this a a bit different but one year we had a family of otters in the rice field we had flooded during the growing season and I would walk the levees checking on the water and find turtles flipped upside down with the bottom of there throat bit/cut. The turtles weren't eatin on they were just flipped over dead. I told my Paw Paw about it and he said he had seen that quite a few times before when he would see the otters move in the fields.
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