Bare bottoms
With bare bottoms you can siphon off detritus including dead organic matter, dead organisms or fish waste that collects on the bottom of the tank. When you siphon, you’re exporting or removing excess nutrients such as ammonia, nitrates, and phosphates. We do not want ammonia in our reef tanks as it is deadly to our reef creatures. High levels of nitrates and phosphates will lessen coral growth and overall color.
With these you can increase the flow by using strong currents to remove detritus and make it much less likely it will collect under a live rock. In time, the wastes move toward your mechanical filtration system and out of your system altogether. SPS corals will benefit from the increasing flow of your currents; if you did this with a sand bed, you’d create an underwater sand storm from your strong currents.
Sand bottom
Sand bed acts as an additional biological filter and another home for good bacteria. Bacteria are responsible for the majority of filtration in your aquarium by removing and recycling excess nutrients by absorbing phosphates and ammonia that is found in fish and invertebrate waste.
A sand bed also provides a food source for corals and other organisms in reef tanks. The sand bed clean up crew, consisting of organisms such as brittle worms, sea cucumbers, and snails, produce such things as eggs and larvae that find their way into the water column, acting as a food source for SPS and other filter-feeding corals.
Although many people believe hydrogen sulfide will migrate up out of the sand bed and poison the tank, a good sand sifting crew will make manual sifting not necessary to control detritus accumulation.