I don't think your dogs were the only culprit here. Dogs+(Lots of water movement+ lots of water surface to air contact=lots of evaporation)= lots 'o missing water.
I wouldn't worry about your dogs drinking it. Dogs have outrageous digestive systems.
So what, a little mycobacterium marinum will get crushed by any healthy dogs digestive system. As long as this water is not sitting on open sores or anything your dogs will be fine. Are you guys fussing over the same animal that eats it's own crap, licks it ass-hole and will pick up any road kill it can find? You must be super paranoid for you dogs. The whole dog drinking out of the toilet thing really happens all of the time and I hope your toilet is dirtier than your tank!