Contrary to what SpaceX has claimed USFWS does not regulate industrial waste water discharge (unsurprisingly). The TCEQ has said they are in violation. FAA has paused launches pending an investigation. Both should have done this many months ago.
In any case with respect to existing contamination the only thing I would trust is an independent third party testing lab testing the water with the data made public. I don't know why you would want anything else.
Industrial waste water permits are not less restrictive than domestic waste water. They could not have "filled in the wrong form" because they need a domestic waste water permit as well.
Also, these permits can't be applied for ahead of time for new technology that is still being developed.
I regularly face this issue in IT circles, where I'm supposed to have a time machine to compensate for the multi-month forewarning everyone else needs.