Most applications you see using bio-balls are for wet-dry sumps. But yes, you could put bio-balls in there. I too use bio-balls fully sub-merged in my second chamber as well. Bio-balls generally float so you may need to keep it down from floating into the other chambers, but this just depends how high the water level ends up. If that were me now, I'd likely get some "Marine Pure" biofilter media/rock - the larger square block. I just like it's form factor sitting in the sump for biofilration growth.