Substrate refers to what you use to cover the bottom of the aquarium. Usually the substrate is purely decorative; however, there are times when one substrate will work better than another. You should always rinse your substrate before adding it to your tank. When buying your substrate, a very general rule of thumb is that one pound of substrate per gallon of water will give you one inch of substrate. For example a 10 gallon aquarium would need about 10 pounds of substrate to achieve a 1” bed.
The most common substrate for freshwater fish tanks is gravel. All sizes of gravel are used in aquariums, but larger gravel will let food drop down in it. This is bad because the food will decompose down, and you can't get to it to suck it out when you do water changes. You also have to be careful not to purchase gravel that is sharp, or it could hurt your fish.
Sand is another substrate option. With sand any debris will stay on top of it, so it is easy to remove from the tank before it decays. Also, some fish prefer sand over gravel. If you get a sand that is to fine your tank will cloud up anytime you or your fish stir up the sand. Also, this kind of sand can get into your filters and cause them to malfunction.
After you make the decision of what kind of substrate you want, you have to decide what color. Darker color substrates better show off the coloration of fish than lighter substrate. Sometimes a darker substrate will make shy fish less timid. The disadvantages of a darker substrate are that is shows fish debris better, so it gets dirty much quicker.
A lot of substrates are calcium carbonate based, which means over time they will raise your PH and hardness. This works out well if you are keeping fish that like harder water with higher PH such as African cichlids, but if you are not keeping fish that prefer hard water then you should not use calcium carbonate based substrates. If you want to test a substrate for calcium carbonate, you can pour vinegar over it. If it bubbles, it is calcium carbonate based and it will raise your PH and water hardness.