The wastes have to be broken down by microbes before the plants can take them up. So the gravel is home to microbes that can use the solid waste as food. As the microbes use the solid wastes, some of them produce the forms of mineral necessary for the plants. The top of the gravel is exposed to light, and so microbes in this area such as algae, are photosynthetic. The mid layers of gravel in the hydroponic are not exposed to light, so the microbes in this area must get their food from other materials, such as fish tank solid wastes.
Water being used to raise fish can make an excellent hydroponic nutrient water.
The wastes from the fish include liquid wastes and solid wastes. The solid wastes from the fish have to be broken down by microbes before they turn into nitrates the plants can use. The microbes that break down the solids should grow in the area of gravel between the surface and standing water. The microbes, once established, will use the fish solid waste as food, to both survive and reproduce. There are bacteria that turn the waste into nitrites and nitrates for plant growth.