Damn man, it's a lil' common sense but hey, I'll fill ya in if you are serious.

A bong's water is it's filter. As the smoke goes through the bong and reaches the water, much of the crap contained in the smoke enters the water, such as tar. The water turns black, smells like ass, and coincidentally, is said to taste like shit.

Don't fret though, your THC won't be able to mix with the water, incase you are thinking you are losing a bunch of THC from your smoke.