Plants are grown as in hydroponics systems, with their roots immersed in the nutrient-rich effluent water. This enables them to filter out the ammonia that is toxic to the aquatic animals, or its metabolites. After the water has passed through the hydroponic subsystem, it is cleaned and oxygenated, and can return to the aquaculture vessels. This cycle is continuous. Common aquaponic applications of hydroponic systems include:

• Deep-water raft aquaponics: styrofoam rafts floating in a relatively deep aquaculture basin in troughs.
• Recirculating aquaponics: solid media such as gravel or clay beads, held in a container that is flooded with water from the aquaculture. This type of aquaponics is also known as closed-loop aquaponics.
• Reciprocating aquaponics: solid media in a container that is alternately flooded and drained utilizing different types of siphon drains. This type of aquaponics is also known as flood-and-drain aquaponics or ebb-and-flow aquaponics.
• Other systems use towers that are trickle-fed from the top, nutrient film technique channels, horizontal PVC pipes with holes for the pots, plastic barrels cut in half with gravel or rafts in them. Each approach has its own benefits.

Most green leaf vegetables grow well in the hydroponic subsystem, although most profitable are varieties of chinese cabbage, lettuce, basil, roses, tomatoes, okra, cantaloupe and bell peppers Other species of vegetables that grow well in an aquaponic system include beans, peas, kohlrabi, watercress, taro, radishes, strawberries, melons, onions, turnips, parsnips, sweet potato and herbs.^{[citation needed]} Since plants at different growth stages require different amounts of minerals and nutrients, plant harvesting is staggered with seedings growing at the same time as mature plants. This ensures stable nutrient content in the water because of continuous symbiotic cleansing of toxins from the water