I'm stumped other than running carbon and a filter sock that is changed often. I did get some KZ coral snow on a whim a few weeks ago. It's said to have similar affects to activated carbon. It clouded up the water big time for several hours but I noticed marked clarity improvements in my water after using it a few times. My sand bed has a bit of algae too which disappeared as well. Might be worth a try. Waiting it out may be the best prescription too, patience. Three months is pretty young for a reef.