Check and make sure there is no cross-contamination of your water supply, as a leaky faucet on a hose standing in water which could back-suck stagnant water into the system.
Boil your water, even bottled water. I have suspected my occasional filtered water binges have caused a bit of gastric unpleasantness.
Also, if you use any kind of water filter, make sure you change it out regularly to avoid bacterial build-up breaking loose and contaminating your water.
Or, as the New Testament suggests, take a little wine for your stomach. Could kill off some gut bugs...God bless!