Shisha smoking is rapidly gaining popularity, especially among the youths, yet knowledge on its toxic effects is limited. While the waterpipe device through which the smoke is bubbling should remove particles and toxic compounds, shisha smoking is still inducing cancers and several acute and chronic diseases. A possible solution to decrease smoke toxicity would be to trap most toxic smoke compounds in the water phase by adding adsorbents, solubilizers and complexing agents such as activated charcoal, cyclodextrins, biomicelles, liposomes and bionanocomposites. Here we discuss flavored tobacco, smoke toxicity, the Low Tox Nargileh, and materials that can be added to the water bowl to decrease toxicity. Further research on the trapping of shisha smoke may also lead to application in various industrial sectors involving smoke emissions.