Isn’t pipe run down a shaft as well, to carry fracking liquid past the water table? The idea being of course to send the liquid down where it is wanted, and not lose any at higher levels. Some people might fear that like overfilling a bottle, frack liquid backs up around the well shaft to the level of the water table. I suppose frack liquid could be pumped in to that point, but it would be way, way more than needed. Adding harmless tracers to the frack liquid and watching for their appearance in the water table ought to answer that question with finality.
The drillshaft is encased by one -- often two courses -- of concrete casing well past the water table. That's in order to block the very circumstance you've posed.