Generally speaking, substantial alterations to hydrological regimes can cause deleterious cascading ecological effects. Just look toward the literature on the hydrological (and consequential ecological) effects of dams (necessary to divert water) for examples.
One of particular interest is dams' tendency to reduce the frequency and severity of flooding events, which are characteristically necessary for much of the functioning of floodplain ecosystems such as those you're describing.
Such reductions can wreak havoc on biodiversity in these regions.
I only meant that the region which has an abundance of water which largely goes to waste can sell their excess via pipelines to the lower 48 wherever there is a dire need.
