I'm gonna quote the chick from my local head shop.

"If you grind your 'tobacco' what you want to do is grab some and roll it into a nice compacted ball and then drop it into the pipe before filling it up. It'll keep the rest of it slipping through and it'll all be fine."

I tried that last night with my new bubbler and it works pretty good. Most the residue in the water was from when I changed the bowl, then I just repeated the whole rolling of the ball before filling it up.

BTW: if you plan to smoke a lot, you might wanna roll a couple of little balls before you start smoking, cause it gets REALLY hard and it seems so time consumig when you're high.