Ever since people started putting fish in saltwater aquariums, there has been a debate not only over what the best material is to use for a substrate, but also over the optimal depth of the sand bed.
Robert Metelsky, the author of Simplified Reefkeeping, recommends a thickness of approximately 1-3/4 to 2 inches, which is about the average depth used in most saltwater aquariums. This substrate depth works well as a pad for live rock and corals as well as giving the tank a "natural" look.
The popular Live Sand Filter (Jaubert/Plenum Filter) is the brainchild of Dr. Dean Jaubert. This innovative filtration system consists of a deep sand bed (DSB) of live sand, a plenum (divider used to make an empty space under the sand) and a protein skimmer. The recommended depth of the sand in a DSB is about 5".
The DSB in the live sand filter depends upon "sand stirrers" moving through the sand, keeping pockets of toxic gasses produced by decaying organic matter from forming. Invertebrates, such as sand shifting sea stars, sea cucumbers, and snails plow through the substrate, consuming detritus and uneaten food as well as releasing the toxic gases (hydrogen sulfide) in small quantities before they can accumulate to dangerous levels. Wrasses, such as the Yellowtail Coris and the Dragon Wrasse, which bury themselves in the sand when frightened or seeking refuge for sleep, also do a great job of stirring the sand, however, they do not consume detritus, as other stirrers do.
Some people believe that a plenum is not required to reduce the nitrate, that the sand at the bottom of the DSB traps the water long enough for anaerobic bacteria to form and begin digesting the nitrate. In an experiment by Robert Toonen and Christopher Wee, they found no significant difference between deep sand beds with or without the plenum to create a void in the sand: both were effective in reducing nitrate.
If you don't have the sand stirrers to consume detritus and uneaten food, as well as keep the substrate free of gas pockets, the sand can turn into a toxic gas factory.
Benefit of a Deep Sand Bed
The benefit of the deep sand bed used as part of a Jaubert/Plenum Filter is that it allows growth of the anaerobic bacteria that convert the nitrate in the aquarium water into a harmless byproduct, nitrogen. Stirring the deep sand bed periodically will prevent other species of anaerobic bacteria from producing toxic hydrogen sulfide. So, as long as your aquarium has sand stirring organisms, or you do the stirring yourself, there is a good benefit of using a deep sand bed for reducing nitrate in the saltwater aquarium.
You Feed Me, I Feed You: Symbiosis. Woods Hole Oceanographic Institution.
Toonen, Robert & Wee, Christopher. An experimental comparison of sediment-based biological filtration designs for recirculating aquarium systems. Aquaculture, vol. 250, no. 1-2, pp. 244-255, 2005. doi:10.1016/j.aquaculture.2005.04.063
Hydrogen Sulfide Toxic, But Manageable. Auburn University Department of Fisheries and Allied Aquacultures.