Insufficient oxygen (environmental hypoxia) may occur in water or substrate, creating a hazardous environment for aerobic organisms and tissue. Deoxygenation increases the relative population of anaerobic organisms such as certain bacteria, resulting in root rot, fish kills and other adverse events. Increasing the concentration of aerobic conditions provides a a healthy hydroculture ecosystem.
Water aeration is required in water bodies that suffer from anoxic conditions. Aeration can be achieved by using an air pump with a diffuser, or by surface agitation from a fountain or spray-like device to allow for oxygen exchange at the surface and the release of noxious gases such as carbon dioxide, methane or hydrogen sulfide.
Dissolved oxygen (DO) is a major contributor to water quality. Not only do fish and other aquatic animals need it, but oxygen breathing aerobic bacteria decompose organic matter. When oxygen concentrations become low, anoxic conditions may develop which can decrease the ability of the water body to support life.
Hypoxia, or oxygen depletion, is a phenomenon that occurs in aquatic environments as dissolved oxygen (DO; molecular oxygen dissolved in the water) becomes reduced in concentration to a point where it becomes detrimental to aquatic organisms living in the system. Dissolved oxygen is typically expressed as a percentage of the oxygen that would dissolve in the water at the prevailing temperature and salinity (both of which affect the solubility of oxygen in water; see oxygen saturation and underwater). An aquatic system lacking dissolved oxygen (0% saturation) is termed anaerobic, reducing, or anoxic; a system with low concentration—in the range between 1 and 30% saturation—is called hypoxic or dysoxic. Most fish cannot live below 30% saturation. A "healthy" aquatic environment should seldom experience less than 80%. The exaerobic zone is found at the boundary of anoxic and hypoxic zones.
Here are ways of infusing air into the nutrient solution and aquaponic tank. Also, keeping the plant roots suspended above the nutrient solution is beneficial, since there is a limit to the amount of oxygen saturation that can be contained in water.
Fountains aerate by pulling water from the surface of the water and propelling it into the air.
This process utilizes air-water contact to transfer oxygen. As the water is propelled into the air, it breaks into small droplets. Collectively, these small droplets have a large surface area through which oxygen can be transferred. Upon return, these droplets mix with the rest of the water and thus transfer their oxygen back to the ecosystem.
Fountains are a popular method of surface aerators because of the aesthetic appearance that they offer. However, most fountains are unable to produce a large area of oxygenated water.
Fine bubble aeration
Fine bubble aeration is an efficient way to transfer oxygen into water. Attached to the unit are a number of diffusers. These bubbles are known as fine bubbles. The EPA defines a fine bubble as anything smaller than 2mm in diameter.
Fine bubble diffused aeration is able to maximize the surface area of the bubbles and thus transfer more oxygen into water per bubble. Additionally, smaller bubbles take more time to reach the surface so not only is the surface area maximized but so are the number of seconds each bubble spends in the water, allowing it more time to transfer oxygen to the water. As a general rule, smaller bubbles and a deeper release point will generate a greater oxygen transfer rate.
However, almost all of the oxygen dissolved into the water from an air bubble occurs when the bubble is being formed. Only a negligible amount occurs during the bubbles transit to the surface of the water. This is why an aeration process that makes many small bubbles is better than one that makes fewer larger ones. The breaking up of larger bubbles into smaller ones also repeats this formation and transfer process. 
One of the drawbacks to fine bubble aeration is that the membranes of ceramic diffusers can sometimes clog and must be cleaned in order to keep them working at their optimum efficiency. Also, they do not possess the ability to mix as well as other aeration techniques, such as coarse bubble aeration.
In certain types of hydroculture, such as flood drain systems, water can be cycled to frequently drain away from the hydroculture system. Plant roots suspended in air provides them aeration that can not be accomplished by allowing plant roots to be saturated in water.
In aquatic environments, oxygen saturation is a relative measure of the amount of oxygen (O2) dissolved in the water. Supersaturation can sometimes be harmful for organisms and cause decompression sickness. Dissolved oxygen (DO) is measured in standard solution units such as millilitres O2 per liter (ml/L), millimoles O2 per liter (mmol/L), milligrams O2 per liter (mg/L) and moles O2 per cubic meter (mol/m3). For example, in freshwater under atmospheric pressure at 20°C, O2 saturation is 9.1 mg/L.
- Tucker, Craig. "Pond Aeration." Pond Aeration SRAC Factsheet 3007
- "Lake Aeration and Circulation" (PDF). Illinois Environmental Protection Agency. http://www.epa.state.il.us/water/conservation/lake-notes/lake-aeration.pdf. Retrieved 13 September 2009.
- Taparhudee, Wara. "Applications of Paddle Wheel Aerators and Diffused-Air System in Closed Cycle Shrimp Farm System." 2002.