When I started reefkeeping 3 years ago, almost everywhere I turned, I was told that bioballs are nitrate factories. Now, I know there are a lot of myths that are passed around and Jimsar's post from Anthony Calfo's book got me thinking that about some of my contributions may be one of those myths circulating the web. In any case, I came across this while I was reading posts at a Canadian site. I've been following this guys posts since he seems quite knowledgeable, his answers concise and factual. I've asked him to look into my system and fine tune my set up.
About bioballs and foam, a quote from Mr. Wilson, our resident expert: "As for the "nitrate factory" question. The idea that any type of biological media will add nitrate to your aquarium is a myth. Man-made biological filtration is redundant, but not harmful.
Nitrifying bacteria populates detritus, not the porous media site (rock, sand, sponge etc.). The ideology of removing the sponge to lower nitrate, would also advocate for a sand and rock-free tank.
Nitrifying bacteria will flourish if there is an abundance of food, namely ammonia and nitrite. If your system is inadequate, you will have nitrogenous compounds build-up and leave a residual of nitrate no matter what you do.
If you remove organic waste before it is converted by nitrifying bacteria, you will not experience a nitrate problem. It's one of those "who came first, the chicken or the egg?" scenarios. In the case of biological filtration, nitrogen compounds (ammonia & nitrite) must come first for residual nitrate to exist.
Proteins such as urea, amino acids, and phenols are converted to ammonia through a biological mineralization process known as deamination. The proper use of chemical filtration such as protein skimming, ozonation, UV sterilization, and physical adsorption (carbon, ion exchangers, polymeric adsorbents etc.), will by-pass the nitrification process and nip the problem of excess organic waste in the bud.
Even without these forms of mechanized filtration, water quality can be managed through the replication of natures balance. A healthy collection of corals and macro algae will reduce organic waste without the need for nitrification. Many successful aquariums are maintained with only a few pumps, artificial lighting and proper livestock selection."