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There was a good article in Scientific American about using the surplus water to saturate crops,
some crops tolerate the excess well, and much of the water gets into the water table.
I have said for a while, that the real problems humans face is energy and fresh water.
If we can figure out effective energy storage, we can solve both problems.
Yes, some crops tolerate water well enough that fields can be flooded for a time at least. The water percolates down to the aquifer, and partially replaces the water that has been pumped out.
Before the San Joaquin valley was farmed and settled, it was pretty swampy, this despite an annual rainfall that would categorize it as a desert. That was due to snowmelt runoff from the Sierras. Now, that water is being used up pretty quickly.
So, yes, energy and water are two real problems. The aquifer under the Central Valley isn't the only one being used up, and there is no practical way to generate energy in sufficient amounts to run an industrialized society without causing some sort of problems.