As quoted before
Bubbling the smoke through water serves to cool down the smoke, which is typically very hot, and to trap some of the heavier and more water-soluble particulate matter, keeping it from entering the smokers lungs.

Most smokers believe that bongs are healthier than other smoking devices; however, a 2000 NORML-MAPS study found that waterpipes filter out more psychoactive THC than they do other tars, thereby requiring users to smoke more to reach their desired effect.