Ground loop when measuring in process pH
This sounds like a combination of problems, probably including grounding.  The main issue sounds like common mode pickup is turning into differential mode signal.  The strategy for dealing with small differential and high impedance signals superimposed on large common mode noise needs to be thought out carefully and considered at every step of the design.  This is not something you add on later to fix the problem.

It would help to see a diagram of your system and proper specs for the pH probe, including the expected signal level and its impedance.

In general, you probably want to treat the probe as producing a balanced differential signal, then have something with very good common mode rejection receive that.  Minimizing common mode pickup, like by using shielded cable, will also be important.  However, shielding without proper balanced signals could do more harm than good.