There are many grow bed media to choose from, ranging from simple ones to 'bioengineered'' branded ones. A very popular and effective one is gravel, which also happens to be very cheap. Gravel is ideal because it provides good support for the roots of the plants and filters the water well. In addition, it proves to be a good habitat for the beneficial bacteria, which will be busy turning fish wastes into plant nutrients. Get round gravel, and it should be big enough not to clog but small enough to provide good root support. The plant roots need good water circulation and oxygen, and if the medium compacts too much, this won't be possible. Good medium size for Aquaponics is around 0.5 to 0.75 of an inch in diameter.

If you opt for another type of medium, you need to ensure that it has some important properties. It should be chemically inert and it must not influence the pH of the water. For example, limestone leaks calcium carbonate and this will push the pH up. Gravel, lava rock, and most river stones are pH neutral. Similarly, the medium should not decompose, as this will affect the pH levels and potentially clog the systems. Decomposing materials can also leak substances in the water that can harm you fish. Avoid soil, peat moss, sawdust or wood chippings.

It is important that the medium you choose is porous, as this will allow for good air and water circulation and will give the bacteria plenty of surface area to colonize. You should also make sure that the medium is easy to handle; it should be gentle on the hands and on the plant's roots.

Now, something about the water. You want the water to be pure, free of chlorine and other chemicals and as close to pH 7 as possible. Municipal water will be of high pH and will contain chlorine. However, all you have to do is to fill your tank and let it sit for two or three days. The chlorine will evaporate off by itself. If the pH of your water is too high, you can buy aquarium pH regulators, or else add in some vinegar or iron sulfate fertilizer. Add small quantities at a time and test. On the other hand, if the pH of the water is too low, get an aquarium pH regulator, add in some baking soda or calcium carbonate. Again, add in small quantities at a time and test. You final pH should be between 6.7 to 7.