The darker the stuff is the more waste has been removed. Here is a contradiction to what you believe
Protein Skimmers - Part 1
What Is Protein Skimming, and How Does It Work?
by Don Carner
Next to primary biological filtration, foam fractionating, better known as protein skimming, is the next most important aspect of any healthy marine system.
Wow, pretty powerful statement, huh? Although there are systems that claim to be "skimmer-free", such as Dr. Jaubert's Live Sand Plenum System, for most of us DOC's (dissolved organic compounds), phenol oils, and other yellowing agents are a nuisance that only active protein skimming can eliminate. Before we jump into the subject matter any deeper, let's discuss how these devices work.
To be as unscientific and as clear as possible, let's simply say that the air bubbles inside the skimmer's body strip the water of undesirable waste by-products. How the bubbles accomplish this is a neat trick that needs some explanation. Ever blow bubbles as a kid? Remember all the rainbow colors on them? Just as the soap clung to the giant bubbles you were creating so too, does all the junk and other organic gunk in your aquarium water. Those pretty rainbow colors were the light refracting off the soap film...you could actually see it! In our skimmers, the bubbles are microscopic and the results can only be "seen" after they burst and deposit their "films" into the collection cup! No pretty rainbow of color here...nope. Only the vilest and nastiest looking sludge imaginable ride our skimmer's bubbles.
How does this happen? It was discovered long ago in waste treatment plants that by injecting high volumes of air bubbles into a column of waste water, the resulting effluent was purer and much cleaner than before. How could this be? Actually, quite simple. Surface tension. Surface tension? Whatzat? The interaction between the oxygen bubble and the surrounding water creates a kind of friction between the two. This friction in turn "charges" the molecules in the water.
Playing on the old Physics Law of "opposites attract", the charged gunk molecules "stick" to the bubbles, riding them up the column of water. Once the bubbles reach the surface air they burst, depositing their hitchhikers into a collection cup. This collection cup keeps the accumulated gunk from slipping back down into the water column inside the reaction chamber. Due to the very nature of saltwater, this process is possible. Freshwater protein skimming just isn't feasible at our level as the technology to make it possible just isn't practical at the hobby level.