Continuing this line of informal research, I was measuring a course in Bermuda when a huge rainstorm came through. Lots of water but the storm passed fairly quickly, and I went to calibrate. There were two huge puddles, each over 1 foot deep for significant portions.
https://plus.google.com/photos.../6003281655414395217
I would guess these large puddles covered about a fifth of the total calibration course length, and I also predicted that they would significantly affect calibration (raising the calibration constant).
Immediately following this aquatic ride I rode over to another calibration course for comparison. Results: "water ride", 2829.5 counts over 250 meters; "dry ride", 2830.13 counts over 250 meters. Not enough difference to talk about; the "dry ride" course is a bit hard to follow as the railway trail snakes just a tad compared to the straight line measured.
If you're wondering why we're using 250 meter cal courses, it's because it is really hard to find a straight-line 300 meters in Bermuda. Laid one out 4 years ago, but one end of that one is now inside a high-security gate near the airport.
In summary, I think that the amount of water I rode through (I just did 2 rides on that occasion!) did not significantly affect the calibration. But what if the whole cal course were under water?? I guess, as Pete and others already said, "further research is needed."
One delightful finding: the Jones-Riegel counter can take a huge plunge and keep on ticking!