Replace water-intensive crop with something more appropriate.
Replace flood irrigation with something like aquaponics which is leagues more water efficient.
Deserts have ecosystems that are adapted to life with limited water. Trying to transplant a crop that evolved with plentiful water into an ecosystem with very little is a bad idea. Even worse is the capitalistic incentive to divert natural watercourse to farm in an arid region.
The thing we should do in this situation is increase our ocean desalination efforts (not to an extent that would counteract sea level rise, but it wouldn't hurt), alongside creating more water pipelines to achieve better distribution into areas which need it. We aren't going to stop crowing crops in desert conditions. It's too effective. We should build more water pipelines to bring water into regions like the California central valley and Colorado and Utah where water is more scarce but crop conditions are good aside from the water availability.