Main water line TDS measurement grounding
I think you are correct, in that the GND is messing with your measurement.

Here are a few options:


Isolate the resistance measurement circuit using opto-isolators and an isloated DC-DC converter.
Compensate for the current leaking to ground by periodically switching off the ground electrode, and measuring the "0" signal. This will give you a resistance to ground which you can remove from your measurement.
Change the sensor installation so the resistance to the undesired GND is greater (put it in a plastic pipe).
You can also move the electrodes closer together, so the leakage is a relatively smaller part of the signal. For example if your signal is ~10ohms, and the parasitic path to ground is ~100 ohms, that will cause a 9% change. If the electrodes were 1/10th the distance apart, and the signal was in the range of 1ohm, the parasitic ground would only cause a change of 1%.