In general US agriculture is extremely wasteful of water. We could drastically cut water consumption by adopting farming techniques used in Israel, but food costs would increase.
I doubt most of the stakeholders paid anything for their water rights. Perhaps, if there is any compensation, it would be equal to what they paid for the actual rates originally inflation adjusted.
Taxes seem like an obvious option. I can't think of any constitutional reasons why they can't tax you for drawing from natural springs, else all new taxes would be a constitutional issue. You may not even need to nationalize then.
You might also be able to simply ban private consumption of water from waterways. Nothing is being seized, they still own the water, it's just worthless because they can't use it. Similar to what would happen if we ban coal. I don't think we'd have to go track down everyone with rights to a coal vein and pay them what it's worth.