When the state gave rights to water to land holders it was well before we had the technology to meaningfully impact water levels and thereby impact other peoples access to water.
Since Roman times land ownership went from the highest heavens to the the deepest deeps, but the law was changed after blimps and other aircraft needed it and they certainly didn't need to pay off millions of people in Italy or anywhere else for that matter.
Same goes for pollution. When there are measurable impacts to other people (ie, my small use, home well went dry and now I need to ship in water at a much higher cost), farmers don't get to claim compensation.
Droughts, floods, dams, and aqueducts are older than any currently standing government. If water rights laws can already consider those events and structures, they can be adjusted to incorporate manmade climate change as well.
Even if all else failed it might well be better to bite the rentier tax once than to live with them forever. Remember takings only requires the payment of fair market value, and these water permits have limited alienability.
I wonder what role "eminent domain" may play in an issue like that.