I'm not familiar with that area, but considering it's not coastal it seems hard to believe the water is simply wasted once it goes into the ground in the lower Colorado basin.
Imperial county is not actually that far from the mouth of the Colorado... Except that, for practical purposes, it does not have a mouth any more, on account of all the water being taken from it.
My guess is that most of what sinks into the ground from agriculture makes its way to a saline aquifer. Some of it may end up in the Salton Sea, which itself is very saline and also shrinking.
