The only way THC can be filtered out in water is by being attached to the tars, since it isn't water-soluble.
http://www.maps.org/news-letters/v05n1/05119wps.html

Due to stems/seeds/leaves having a higher tar content than buds do, it's possible that the studies that have shown that water filters out more THC than tars is because those were used instead/in combination with the buds. This is only a guess, but if that's true then smoking cannabis correctly (buds only) would most likely prove the opposite, and is probably the reason why water pipes are shown to be effective. Regardless, I get fucking blazed off of bongs... much moreso than pipes, meaning I will continue using water filtration as much as possible.