When you say it's getting clogged, do you mean it stops flowing, or it clumps together ?
If it stops flowing, I'll guess it's because every time you restart your pump and it rises to the top, all the fine stuff is plugging up either your sponge or the line itself.
As suggested above, try running your reactor with it's own/dedicated pump.
Or, buy a mesh bag
like this and rinse out all the fine stuff before filling your reactor.