Oxygen and carbon dioxide dissolve in water, and most fishes exchange dissolved oxygen and carbon dioxide in water by means of the gills. The gills lie behind and to the side of the mouth cavity and consist of fleshy filaments supported by the gill arches and filled with blood vessels, which give gills a bright red colour. Water taken in continuously through the mouth passes backward between the gill bars and over the gill filaments, where the exchange of gases takes place. The gills are protected by a gill cover in teleosts and many other fishes but by flaps of skin in sharks, rays, and some of the older fossil fish groups. The blood capillaries in the gill filaments are close to the gill surface to take up oxygen from the water and to give up excess carbon dioxide to the water.

Most modern fishes have a hydrostatic (ballast) organ, called the swim bladder, that lies in the body cavity just below the kidney and above the stomach and intestine. It originated as a diverticulum of the digestive canal. In advanced teleosts, especially the acanthopterygians, the bladder has lost its connection with the digestive tract, a condition called physoclistic. The connection has been retained (physostomous) by many relatively primitive teleosts. In several unrelated lines of fishes, the bladder has become specialized as a lung or, at least, as a highly vascularized accessory breathing organ. Some fishes with such accessory organs are obligate air breathers and will drown if denied access to the surface, even in well-oxygenated water. Fishes with a hydrostatic form of swim bladder can control their depth by regulating the amount of gas in the bladder. The gas, mostly oxygen, is secreted into the bladder by special glands, rendering the fish more buoyant; the gas is absorbed into the bloodstream by another special organ, reducing the overall buoyancy and allowing the fish to sink. Some deep-sea fishes may have oils, rather than gas, in the bladder. Other deep-sea and some bottom-living forms have much-reduced swim bladders or have lost the organ entirely.

The swim bladder of fishes follows the same developmental pattern as the lungs of land vertebrates. There is no doubt that the two structures have the same historical origin in primitive fishes. More or less intermediate forms still survive among the more primitive types of fishes, such as the lungfishes Lepidosiren and Protopterus.

The circulatory system

The circulatory, or blood vascular, system consists of the heart, the arteries, the capillaries, and the veins. It is in the capillaries that the interchange of oxygen, carbon dioxide, nutrients, and other substances such as hormones and waste products takes place. The capillaries lead to the veins, which return the venous blood with its waste products to the heart, kidneys, and gills. There are two kinds of capillary beds: those in the gills and those in the rest of the body. The heart, a folded continuous muscular tube with three or four saclike enlargements, undergoes rhythmic contractions and receives venous blood in a sinus venosus. It passes the blood to an auricle and then into a thick muscular pump, the ventricle. From the ventricle the blood goes to a bulbous structure at the base of a ventral aorta just below the gills. The blood passes to the afferent (receiving) arteries of the gill arches and then to the gill capillaries. There waste gases are given off to the environment, and oxygen is absorbed. The oxygenated blood enters efferent (exuant) arteries of the gill arches and then flows into the dorsal aorta. From there blood is distributed to the tissues and organs of the body. One-way valves prevent backflow. The circulation of fishes thus differs from that of the reptiles, birds, and mammals in that oxygenated blood is not returned to the heart prior to distribution to the other parts of the body.