The same crops can be grown cheaply elsewhere. Artificially subsidizing California agriculture with unsustainably cheap water undercuts growers in other markets.
Stop giving insanely cheap water to large growers with inefficient water usage practices, and the market will quickly right itself and move production elsewhere. At a more sustainable price, with less ecological imbalance.
For some reason, the same utilities in California sell the same water for agricultural use for 1/20 - 1/10 the price as they sell it to residential or commercial users. To me, this screams inefficiency.
I suspect that agricultural users are being charged too little, and so they have too little incentive to be efficient. (Or they are pumping groundwater and paying nothing.) And residential users are being charged more than the service really ought to cost.
The only semi-legitimate justification I can come up with is that there are fixed costs associated with water users, and each residential user uses much less water than an agricultural user. But there are better ways to handle this.