I have treated my whole reef with the combination med. It is reef safe, but you lose feather dusters and some bristle worms in addition to your shrimps, crabs and copepod population. Your clam will be fine. It is painful at first, but in the long run if you have a mature tank with SPS and want to keep them healthy you need to treat the whole system. I recommend replacing a portion of the live rock after you are done. I don't have proof, but I think you lose some beneficial bacteria when you treat the whole system.