Several substrate options exist to choose from when you're setting up your aquarium. Gravel and marble are two popular choices. Gravel has been a staple aquarium substrate for years, but many hobbyist are starting to use glass marbles. Both substrates have pros and cons; depending on how you plan on setting up your aquarium, which substrate you choose may determine how you maintain your aquarium.
Type of Filter
Depending on the type of filtration system you use in your aquarium, the type of substrate you should use will vary. For example, gravel works better than marbles with under-gravel filters, but marbles will be fine in an aquarium if you have a hanging filtration system. Canister filters and hanging filters do not need substrate to work properly, whereas under-gravel filters draw the water down, trapping microbes, bacteria and detritus in the gravel. You can occasionally clean them away with a gravel vacuum during regular aquarium maintenance.
Gravel
Gravel works best for most aquariums, no matter what size. There are different types of gravel that you can choose from, and a wide range of colors if you opt for regular aquarium gravel. Pea-size gravel or basic aquarium gravel has a larger surface-to-volume ratio than marbles; and good bacteria need the surface area to colonize so they can properly break down waste. Smaller gravel can become impacted, leaving fewer spaces for bad bacteria to thrive.
Marbles
Glass marbles come in a wide range of colors, sizes and shapes -- they're not always spherical -- but no matter what size, they create large gaps where excess food and fish waste can accumulate. This waste will build where your bottom feeders cannot reach, which will cause algae growth and overall water quality problems. You can use a regular gravel vacuum on marbles, but you will have to do so frequently. On the other hand, if you are breeding fish, marbles can be a good substrate because the gaps provide protection and coverage from adult fish who would like to eat the fry.
Adding Decoration and Plants
If you're wanting to add plants and decoration to your aquarium, you may find the substrate you choose can make a difference. Caves, castles and other heavy decor can sit right on marbles, but plants won't fare well with marbles. Fake plants can easily be buried and held down in gravel, and live plants can take root in gravel substrate.