Use a hot glue gun, it works wonders...or if you want something less messy, use a silicone-based sealer (kinda like caulk, I dunno if you like the caulk or not) Make sure its silicone based, and try not to get any inside the bong if you can...it'll be smelly and unpleasant. Make sure you let it cure, might take a day or two to fully seal the gaps.

What kinda bong is it? are there joints between materials/pieces of the bong that have the non-airtightness?