They can remove a fair amount of nutrient from the water if left running too long. In turn they may affect the food the bacteria need to feed on but they will not remove the bacteria. As long as the filter is only used occasionally to polish the water, you should be just fine. Best suggestion is run it when you do your weekly maintenace to clean the glass, blow off the rock or doing water changes. It will catch any floating detritus that rises. Don't use it 24/7 though.