Available water belongs to the public, not landowner. However, water use rights are assignable.
The right to use water goes first to the person with the oldest claim (the "senior appropriator"). You might have no claim to water running through your land, or as a junior appropriator only get access during wet years.
You may not block a senior appropriator from being able to make their appropriated beneficial use of that water.
As regarding pristine or pollution, quoting the NM constitution, 'The protection of the state's beautiful and healthful environment is hereby declared to be of fundamental importance to the public interest, health, safety and the general welfare. The legislature shall provide for control of pollution and control of despoilment of the air, water and other natural resources of this state, consistent with the use and development of these resources for the maximum benefit of the people.'
I'm not a water rights lawyer. Florida water law is very different from New Mexico. I do not know if the NM legislature has passed laws allowing cities to pass stricter pollution laws.
That said, if your phosphate mine's tailings pond wasn't built to handle the expected consequences of a hurricane, failure to handle said hurricane is no excuse for negligence.
What you describe now has nothing to do with a river and can no longer be called 'pollution'. For one, storm surge flooding has been around long enough that the ecosystem has adapted to the occasional event, making it part of the pristine state.