That is a very interesting point to raise.
I would think that the only formal wells would have been found at the larger farms and villages; La Haye Sainte, Hougoumont, Plancenoit, etc. After the heavy rains there would doubtless have been some standing water in the ditches, but not very palatable, and probably dried away by afternoon.
Another question to ask along those lines would be under what circumstances the men would be allowed to fall out to fill their canteens; as I recall the various memoirs state the terrible thirst they suffered, I would think that no one was allowed to fall out in search of water.
When I think of canteens at Waterloo I am always reminded of Captain Mercer's wandering bombardier who rejoined the troop with his men, every one of whom had a canteen full of runm, but "quite sober!". (Mercer's italics and exclamation mark; Journal of the Waterloo Campaign, p. 159 in my paperback edition, 1995.)
Whether it was 'baptised' or not, rum was certainly not the ideal thirst quencher, but it was perhaps a real benefit to the men who had to bear that day.