Fish use the oxygen dissolved in the water for respiration. This dissolved oxygen (DO) is gas in simple solution (not the covalently bound oxygen in the water molecule). Fish extract this oxygen with their gills. Water has relatively little DO (<14 mg/L) compared to the oxygen (240 mg/L) in air, so fish must be efficient in getting it. One factor that contributes to this efficiency is the unidirectional flow of water through their gills. Terrestrial animals have bidirectional flow (in and out of the same tube, the trachea) which is inefficient in that fresh inspired air mixes with stale expired air. With unidirectional flow, there is no mixing. Another factor is the countercurrent movement of blood and water. At the lamellae, blood flows one way and water the other, which insures that maximum gas exchange will occur. If water and blood moved parallel with one another there would be less gas exchange
While the quantity of oxygen is low in water, the partial pressure (PO2) of oxygen may be the same as in the air. If so, the water is said to be at "air saturation", or simply, "saturation", because all of the oxygen that the water can hold is in solution. When respiration of fish and bacteria have reduced the amount of oxygen in the water, the partial pressure will be below that of air. Depending on species, when water falls below 25-50% saturation, fish have difficulty getting enough oxygen and may suffocate. When water is below saturation, the partial pressure differential tends to move oxygen from the air into the water, which is the basis for aeration. Under unusual circumstances water may be supersaturated, in which case oxygen moves from water to air.
For every molecule of oxygen consumed by respiration, there is a molecule of carbon dioxide produced. Carbon dioxide is much more soluble in water than oxygen so blood can hold the amount produced with very little increase in partial pressure. That means that there is a very small pressure gradient between blood and water to push it out of the body. In order to rid themselves of carbon dioxide, fish use some physiological tricks including the use of carbonic anhydrase. Despite this low gradient between blood and water, fish in nature have little problem moving carbon dioxide out of their bodies. In recirculation aquaculture, however, carbon dioxide can reach extraordinarily high levels in the water causing fish distress. This is particularly a problem when liquid oxygen is used instead of atmospheric aeration to provide oxygen (during standard aeration carbon dioxide is lost as oxygen is gained).