This is the question we get asked the most about in sump protein skimmers, there really is no set depth that the skimmer needs to run in besides the pump should be covered with a minimum or 1″ of water about the highest point on the pump. All of our skimmers have a suggested water level that we have tested and found allows the skimmer to work most efficiently. The lower the water level the greater the air vacuum will be in most cases. But if you run the skimmer too shallow and close the valve too much just to gain a collection you will loose efficiency of the skimmer and will be more susceptible to overflows. If the water level is too high you loose range of control and may overflow.