So, with the source controlled (I'm guessing you've stopped the leak) and knowing there's gravel (i.e., quartz) I worry about the foundation concrete as well. I'm thinking the potable water supply is protected by the clay (i.e., there's no effect to human health of the environment), you may be able to address low pH using hydrogen peroxide, which should yield water and sulfur (I'm not really a chemist, but think it'd work like this).
Regarding settlement if the facility has been there for some measure of time, the fill's not likely a bad actor. If this is a newish facility that sprung a leak, I'd consider poorly-compacted fill leading to settlement and see if that could result in a leak.
I like guess work from the comfort of cyberland!
Good luck.
f-d
¡papá gordo ain’t no madre flaca!