All the filter media will do is provide a breeding ground for nitrates. I see no benefit of keeping it in there. However I'm considering runnig it for a couple days w/ a little activated carbon (phos free) just for a little cleansing. I had LR rubble inthe filter for a while but even that was building up detritus. In a tank of this size (or lack there of) it's pretty hard to afford some of those "luxuries". That sort of thing can just as easily foul up the water.