This is a rather common question we get asked about for in sump protein skimmers, there really is no set depth that the skimmer needs to run in. The two things you need to look for is that the pump is covered with at the minimum or 1″ of water about the highest point on the pump and second is that the water level in the sump is below the water outlet pipe on the skimmer. You want to see the water flowing out of the skimmer and drop down into the sump water.