Running carbon is fine. Some say you should only run it with carbon for a week once a month and others leave it in there for 24/7. I think one of the worries is that the carbon could start leaching out bad stuff if it's not replaced after a period of time. I use chemi-oure and mine stays in. Also make sure the carbon is for saltwater. I see some carbon state for freshwater only. I'm not sure what the diference is.