pH sensor ground loop alike problem
Key phase here: Switched mode power supply. I'll bet your having an RF problem. Your power supply stinks and is conducting RF onto your PCB and that is causing your sensor to function like an antenna. And the RF pathway is even better when you stick the sensor in water. RF problems are weird, its an art not a science because if its really high frequency above 100MHz, measuring it with even an oscilloscope probe or moving a cable can change the preferred pathway for the signal. 

Stick a voltmeter between the sensor and the water, do this for DC and AC mode, also check everything with an oscilloscope. If you have a spectrum analyzer with a near field wand that would be great too. 

What can you do? Make sure you isolate your analog electronics from bad things. Use shielding, ferrites and low pass filters to keep signals out of your sensor that you don't want. Follow good PCB practices. Even digital sampling of the ADC can change your signal.

If its not an RF problem, its a ground loop problem, and by ground we are talking very small currents, like pA's of current, like the kind your amplifier will pick up. There are pA's of current flowing everywhere. I doubt this is the problem but something to think about