Sure, 90% is an overestimate of the portion of water applied for irrigation that returns as recharge to the groundwater system.
However that number is not zero in the Lower Colorado River basin. I work in groundwater modeling for various clients in the desert southwest, the number we assume for agricultural return flow recharge varies based on crop type and other factors. 90% is an overestimate, 0% is an underestimate
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.
That's not the case in the lower Colorado basin. If it was, there would not be a problem.