Choosing An Aquarium Substrate

There are a number of different choices when it comes to choosing what to do with the bottom of the tank.

When choosing bare bottom people are usually doing so because of the higher level of control they have over nutrient levels in the water.
By removing the substrate you also reduce the amount of potential detritus buildup.
It is a popular choice when the tank is primarily hosting stony corals because sps corals prefer close to pristine conditions. This however should not be confused with low nutrient levels. A natural reef has a huge amount of food available. But unlike our aquariums there also exists an eqully huge number of organisms eating the food. In our tanks we tend to have a tough time maintaining species variety and numbers so our excess food is allowed to break down into nitrates and phosphates.
In a sps dominated reef aquarium the turnover rate can be in excess of 100x meaning the total volume of aquarium water is moved 100 times in one hour through return pumps, powerheads or other means of water movement.
With this amount of water movement the tank can be one big dust cloud if a fine sand bed is applied.
When choosing this type of tank naturally you will not be able to host livestock such as
sand sifting cucumber and fighting conches.

Shallow sand beds are a way to attain a pleasing look, usually around one inch deep while keeping cost low.
This type of sand bed does not perform well for filtration but does allow the reefer to keep sand sifters.

A deep sand bed is good for managing nutrients. It is typically between four and six inches deep.
Nitrate will be processed by anaerobic bacteria and get exported as a gas.
This type of sand bed will provide a good habitat for various micro fauna as well. Just be careful that the sand bed is never stirred, if this happens anaerobic zones in the sand bed will be releasing a very destructive amount of waste into the water column. The tank will very likely crash.
I am personally utilizing deep sand beds. They increase the overall species variety, thereby providing natural food for fish and coral and in addition my live rock tends to look more alive because I don't have to starve the tanks. The life, bacteria, pods, worms and stars etc. can manage quite heavy feedings without the consequence of high nutrient levels and the algae that typically follows.

If you decide to go with something other that a bare bottom you will have a large number of substrate choices.
The range goes from crushed coral to fine sand.
Typically a new reefer will go to a pet store and take the advice he can get from the store. Typically he will live to regret taking the advice from the store.
There is a great deal of really bad advice coming from the fish stores unfortunately. Personally I have wasted a lot of money on filters, lights and pumps that were not really what I needed. It was however what the store thought I needed and I took their advice.
I have to admit that impulse purchases and bad equipment decisions are mostly my own fault, I should have studied my choice more before buying.

I do feel however that when it comes to the choice in substrate that the advice from the stores usually could be much better.
Very often you will hear that crushed coral is the best choice and this substrate is also what you often will see covering the tank bottoms at the fish store. Naturally a newbie reefer will think that crushed coral is the way to go.
At this point the newbie reefers really need to stop and think. First, any kind of substrate will work. Some better than others but they WILL all work. This means that you can actually choose the kind of substrate you like the best. It doesn't matter what the store owner has in his tank at home, it doesn't matter when he tells you that his substrate is the best in the state. At this point, before the actual purchase all that matters is what you think will make your own reef look its absolute best.

Now that this point has been made I will try to explain why the store owner is wrong.
Crushed coral is very coarse and when you have food and feces breaking down in the tank you don't want areas in your tank that snails, hermit crabs or cucumbers etc. can not easily clean. Crushed coral collects detritus and in some cases the coarse substrate can injure corals placed on the sand bed such as open brain corals.
When the store puts crushed coral in their tanks usually there will only be enough to barely cover the tank bottom.
With this amount of crushed coral it is fairly easy to keep it clean, simply wave a hand around and siphon out the floating particles.
This can be done with no harm done to corals or fish that is being cared greatly for.
I chose a shallow sand bed. It is about two inches deep and made of aragonite, the grain size is too large for my taste, but it is very difficult to remove and replace the sand bed of an established reef tank. Imagine having a crushed coral bottom and realizing too late that it is accumulating huge amounts of detritus. Now you almost have to replace it.
For my next setup I will go with either a bare bottom tank or a deep sand bed of fine sand. I will only choose the bare bottom setup if I at the time will have a heavily stocked sps tank because I prefer the look of a sand bed.