I have never knowingly had water in fuel tanks but a colleague of mine had a (temporary) loss of thrust on an engine after take-off after collecting a 737 that had been on the ground for over a week in the UK for a repaint. I was collecting the next one and was given an engine run up procedure by Boeing to ensure that any water had been drawn through the lines before we got airborne.
On another occasion when I was waiting for a paint job to finish I got talking to a 737 crew who ferry aircraft all over the world. I mentioned the issue and they said that they had never experienced it and they had picked up aircraft that had been in storage in the desert for over 2 years! Maybe it is a local climate thing or maybe they drain off any water after long term storage.
S&L