Holy Dog Water!

I think that the answer to this lie deep within the canine psyche. Back when they were first being tamed dogs would fight for dominance of their semi-domesticated pack.
Now, back then the dog that was the leader (the Alpha male) would often try to cement his claim by showing the other dogs how tough he was. One way he would do this is by showing his control over the food supply of the rest of the pack. in the wild, this would simply mean that h would chose when the hunted and who they hunted.
But as domesticated animals, all of the food was given to them by their human masters, so they needed to find a new way to exert their dominance.

Now, based on the findings in the Meänkieli "Dog Burial Grounds", we know that they were fed using crude bowls made of stone or of wood, in fact, a petrified half-coconut was found on the site as well. Judging by the fact that the lighter containers such as the coconut were upside-down when they were covered (and RC-dating revealed that there were large piles of bacteria (which were normally found in water) as well ground up caribou (which some believe may be a precursor to modern day kibble) that the Alpha dogs would knock over food bowls to show that they were still the leader of the pack

now, there are two ways to solve this problem (both work very well, and were developed directly from these discoveries).

The first is to show your dog that you are the "Alpha" dog, this can be very difficult, you might want some help form a local dog trainer

the second is to purchase a stone bowl (or even better yet, a coconut) and place it next to your dog’s water dish, without fail, they will knock over the "natural" bowl and leave the normal bowl alone

It’s a rather common problem, I believe "Dog Fancy" wrote an article about it in their 2007 April issue