Are you going to plant it? If so, that will help, especially plants the develop large rootmasses, like swords. Otherwise, IMO, you'd be better off stocking it with an aquatic worm that will do the work for you--black worms, maybe? There are a few species out there. The problem is not that stagnant areas will develop, but that will be disturbed after developing. The digging of the puffer should prevent much of that, especially if he's encouraged to root around for critters.