idk, i can totally see where you're irritated, HOWEVER, i feel that as parents, we should NEVER allow our children to have pets unless we are planning to bear the ultimate responsibility of the critters basic needs. so, it doesn't sound like you are even almost leaning in that direction, but please don't allow the animals to suffer and not fill up the water bottle yourself if that is the only option available at the time(like the kids are not at home to do it).
twice in several months is really not that frequent, it's not like you're finding the water bottle empty every morning, however, twice in several months is probably twice too many for the thirsty little critters :( your kids are not babies, i'd sit them down and lay out the consequences. next time i find the water bottle empty, this is what's going to happen: the pets are gone, you each owe me $5 for giving them water, you have to do extra chores, whatever consequence it is that YOU feel is appropriate and will actually follow through with. beyond that, maybe try to integrate checking that animal's food/water situation into their daily routine. in the morning, one of them checks food/water when brushing teeth, in the evening, the other child is responsible for checking food/water levels.
sounds like you're working hard to teach your children responsibility and compassion when caring for animals - i applaud you for that!