my baffles are all the same height. 10" and the water in my sump/refuge is 10 in so that it can flow over each baffle, except in the last compartment where the pump is of course. i have one "bubble trap" where I put one 10" peice of glass flush on the bottom of the fuge and the next piece of glass an inch off the bottom and then the next piece of glass right on the bottom again. This makes the water travel over then under and then over again which help eliminate bubbles.