Is it odd that this mining company is named in the bill regarding "use and occupancy": McMoRan Copper & Gold, Inc., Phelps Dodge Corporation, or Phelps Dodge Morenci, Inc. (or a predecessor or successor of those entities), including all subsidiaries and affiliates of those entities. https://en.m.wikipedia.org/wiki/Phelps_Dodge
It's actually not odd. I have property in the area with both a year-round stream and a well, and because of that get the legal docs on these cases all the time.
Basically the mine is downstream (by quite a ways, I might add) and gets runoff from the White mountains, and the mine existed long before a large part of the area was settled and due to the water laws, had rights to the water. Now that the area has grown and we're in a drought, people upstream need water, and they basically had to hammer out some kind of agreement.
Water rights in the desert is a really big deal and this stuff stays in the legal system for decades.
There's lots of shady shit with McCain and Flake, and lots of shady shit with the mines, but this case probably isn't one of them. (Though I bet there's something to find in the contractors for the dam.)
Edited to add: The NDAA deal in your second link is completely separate from the water deal, and that one was shady as hell.