Hi, I talked to the vet treating these horses. While they have botulism, it did not come from any water reaching the hay. In fact, water did not reach the hay. The vet is positive there was another source of infection.
Obviously, if bags of feed or hay got wet, it would mold and you would need to dispose of it. But botulism is not a result.
Years ago I remember a story about a couple of horses dying. There was a dispute about what killed them - the local sewage treatment plant had overflowed untreated wastewater onto their pasture, but their pasture was also heavily overgrown with star thistle (poisonous). Ultimately the star thistle was blamed for the deaths (although of course the owner thought the sewage treatment plant was the real culprit).
I'm curious as to whether the flood created any situation that permitted the botulism organism to thrive in an area where the horses could ingest it, and/or how they ingested it. FD can you keep us posted?
According to Dr. DeLisle, there should be no lasting effects on pastures even if they were flooded, as far as cutting and baling hay off them. Botulism in hay often come from a dead animal being rolled up in a bale so always check hay before feeding, she says. (Not sure how you'd do that on a big round bale).
Of course, if there is any debris in the field or fences down, etc., you need to get that out of pastures.
If your horse was standing in water or has been in muddy conditions, she suggest treating pre-emptively for thrush and keeping a watch out.