Aquatic respiration is the process whereby an aquatic organism exchanges respiratory gases with water, obtaining oxygen from oxygen dissolved in water and excreting carbon dioxide and some other metabolic waste products into the water.

In very small animals, plants and bacteria, simple diffusion of gaseous metabolites is sufficient for respiratory function and no special adaptations are found to aid respiration. Passive diffusion or active transport are also sufficient mechanisms for many larger aquatic animals such as many worms, jellyfish, sponges, bryozoans and similar organisms. In such cases, no specific respiratory organs or organelles are found.

Although higher plants typically use carbon dioxide and excrete oxygen during photosynthesis, they also respire and, particularly during darkness, many plants excrete carbon dioxide and require oxygen to maintain normal functions. In fully submerged aquatic higher plants specialised structures such as stoma on leaf surfaces to control gas interchange. In many species, these structures can be controlled to be open or closed depending on environmental conditions. In conditions of high light intensity and relatively high carbonate ion concentrations, oxygen may be produced in sufficient quantities to form gaseous bubbles on the surface of leaves and may produce oxygen super-saturation in the surrounding water body.

All animals that practice truly aquatic respiration are poikilothermic. All aquatic homeothermic animals and birds including cetaceans and penguins are air breathing despite a fully aquatic life-style.

Echinoderms have a specialised water vascular system which provides a number of functions including providing the hydraulic power for tube feet but also serves to convey oxygenated sea water into the body and carry waste water out again. In many genera, the water enters through a madreporite, a sieve like structure on the upper surface but may also enter via ciliary action in the tube feet or via special cribiform organelles.

Molluscs commonly possess gills that allow exchange of respiratory gases from an aqueous environment into the circulatory system. These animals possess a heart that pumps blood which contains hemocyanin as its oxygen-capturing molecule. The respiratory system of gastropods can include either gills or a lung.

Aquatic arthropods generally possess some form of gills in which gas exchange takes place by diffusing through the exoskeleton. Others may breathe atmospheric air while remaining submerged, via breathing tubes or trapped air bubbles, though some aquatic insects may remain submerged indefinitely and respire using a plastron. A number of insects have an aquatic juvenile phase and an adult phase on land. In these case adaptions for life in water are lost at the final ecdysis. A number of orders of insects such as mayflies, caddis flies and stone flies have aquatic juvenile stages while some orders such as Lepidoptera have just a few examples such as China mark moths. A very few arachnids have adopted an aquatic life style including the diving bell spider. In all cases, oxygen is provided from air trapped by hairs around the animal's body.

Most fish exchange gases using gills on either side of the pharynx (throat), forming the splanchnocranium, the portion of the skeleton where the cartilage of the cranium converges into the cartilage of the pharynx and its associated parts. Gills are tissues which consist of threadlike structures called filaments. These filaments have many functions and are involved in ion and water transfer as well as oxygen, carbon dioxide, acid and ammonia exchange. Each filament contains a capillary network that provides a large surface area for the exchange of gases and ions. Fish exchange gases by pulling oxygen-rich water through their mouths and pumping it over their gills. In species like the spiny dogfish and other sharks and rays, a spiracle exists near the top of the head that pumps water into the gills when the animal is not in motion. In some fish, capillary blood flows in the opposite direction to the water, causing countercurrent exchange. The muscles on the sides of the pharynx push the oxygen-depleted water out the gill openings. In bony fish, the pumping of oxygen-poor water is aided by a bone that surrounds the gills called the operculum.