XT600 and deep water
 

You need to T off the carb breather pipes - it's described higher up in the thread and confirmed by Chris Scott in post 12. I have mine raised to the frame rails below the seat and regularly cross rivers and fords that are spark plug height with no issues at all. Before doing this mod (when I first got the bike) it would do exactly what you describe.

Ah! For some reason, I thought it was about another problem! I was so concentrated at my temperature issue, and so convinced that the engine did not sucked water in, that the carb breather pipes issue looked liked another problem.

But in fact it could well be the exact same problem! In fact one simple test should make things clear. Putting the breather pipes into a glass of water, would shut the engine down (This said, without knowing how that part of the bike looks like).

Currently I am ill and in bed. But as soon as I can, I Will try this out. Thanks!