Most people assume the gravel, or substrate, is only there to make their aquarium more attractive. If that is the case, is it a necessity or not? The answer is that it is not an absolute requirement, but there are many reasons why it's recommended. There are also situations in which substrate isn't desirable.
Perhaps the most important function that gravel serves is to provide a home for beneficial bacteria.
Those bacterial colonies are necessary to eliminate waste produced by the fish, leftover food, and plant debris in the aquarium. If the bacteria don't have a comfy gravel bed to live in they will find other places, but may not grow in sufficient quantities to keep the aquarium safe for your fish.
If the tank is left with a bare bottom, it will be necessary to change the water more often in the aquarium to keep harmful wastes from building up. In the event the tank is heavily stocked, even frequent water changes may not be enough to keep ammonia and nitrites at bay.
Gravel of the appropriate type (i.e.: not too bold and glaring) can create a pleasant habitat for your fish. The more comfortable the habitat is for your fish, the less stressed and more healthy they will be. Stress is a major contributor to a compromised immune system in fish, leaving them more susceptible to diseases.
Substrates can provide a safe home for eggs laid by fish. Large-sized substrates allow the eggs to drop out of reach of hungry adult fish who wouldn't hesitate to eat their own offspring. Likewise, the infusoria that may be harbored in the gravel bed, is a good first food for fry.
In addition to reducing stress on the fish, substrates can also be used to improve the chemistry of the water.
If you have live plants, substrate is critical, and second only to lighting in keeping your plants alive. The proper substrate in planted tanks can ensure your plants root well, have their nutritional needs met, and have a long and healthy life.
Last but not least, substrates can provide aesthetic appeal for the owner and others who view the tank. Substrate hides the debris that inevitably is produced every day within the tank. Try having a bare bottomed tank for even a day, and you'll be amazed at how much 'junk' appears on the bottom.
In addition to hiding undesirable things, substrate shows off what you really want to see. A silver fish against bare glass doesn't stand out but put a dark gravel on the bottom and suddenly the fish stand out.
When Substrate Isn't Ideal
Occasionally there are situations in which substrate isn't necessary, or even desirable. The primary one is in a grow-out tank that is used to hatch eggs and raise young fry. Grow out aquariums must be kept scrupulously clean, and require frequent water changes as well as prompt vacuuming away of waste and uneaten foods.
Fry are so tiny that it is often difficult to distinguish then if they are against a gravel substrate. It is all too easy to suck them up when vacuuming the substrate, or changing the water. A bare-bottomed tank makes it far easier to spot small fry, and thus avoid them when cleaning the tank.
Hospital tanks also may not have substrate, which can harbor parasites that can linger there and infect the next inhabitant. A bare-bottomed tank is a good way to avoid that possibility. For the same reason, some owners choose to leave quarantine tanks bare-bottomed as well.