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.
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.
That would be true if there was a "water rights law". The problem is that there is no single law. Water rights are tied to real property law, especially when farming is involved. The American legal tradition, as adopted from the brits, places the property owner as a king on his land. It has great trouble allowing others, non-landowners, to tell that king what he can and cannot do with his land.
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.