The advent of jaws allowed fish to eat a much wider variety of food, including plants and other organisms. In fish, food is ingested through the mouth and then broken down in the esophagus. When it enters the stomach, the food is further broken down and, in many fish, further processed in finger-like pouches called pyloric caeca. The pyloric caeca secrete digestive enzymes and absorb nutrients from the digested food. Organs such as the liver and pancreas add enzymes and various digestive chemicals as the food moves through the digestive tract. The intestine completes the process of digestion and nutrient absorption.
Most fish exchange gases by using gills that are located on either side of the pharynx. Gills are made up of threadlike structures called filaments. Each filament contains a network of capillaries that allow a large surface area for the exchange of oxygen and carbon dioxide. Fish exchange gases by pulling oxygen-rich water through their mouths and pumping it over their gill filaments. The blood in the capillaries flows in the opposite direction to the water, causing counter current exchange. They then push the oxygen-poor water out through openings in the sides of the pharynx. Some fishes, like sharks and lampreys, possess multiple gill openings. However, most fishes have a single gill opening on each side of the body. This opening is hidden beneath a protective bony cover called an operculum.
Many fish can breathe air. The mechanisms for doing so are varied. The skin of anguillid eels may be used to absorb oxygen. The buccal cavity of the electric eel may be used to breathe air. Catfishes of the families Loricariidae, Callichthyidae, and Scoloplacidae are able to absorb air through their digestive tracts. Lungfish and bichirs have paired lungs similar to those of tetrapods and must rise to the surface of the water to gulp fresh air in through the mouth and pass spent air out through the gills. Gar and bowfin have a vascularised swim bladder that is used in the same way. Loaches, trahiras, and many catfish breathe by passing air through the gut. Mudskippers breathe by absorbing oxygen across the skin (similar to what frogs do). A number of fishes have evolved so-called accessory breathing organs that are used to extract oxygen from the air. Labyrinth fish (such as gouramis and bettas) have a labyrinth organ above the gills that performs this function. A few other fish have structures more or less resembling labyrinth organs in form and function, most notably snakeheads, pikeheads, and the Clariidae family of catfish.
Being able to breathe air is primarily of use to fish that inhabit shallow, seasonally variable waters where the oxygen concentration in the water may decline at certain times of the year. At such times, fishes dependent solely on the oxygen in the water, such as perch and cichlids, will quickly suffocate, but air-breathing fish can survive for much longer, in some cases in water that is little more than wet mud. At the most extreme, some of these air-breathing fish are able to survive in damp burrows for weeks after the water has otherwise completely dried up, entering a state of aestivation until the water returns.
Tuna gills inside of the head. The fish head is oriented snout-downwards, with the view looking towards the mouth.
Fish can be divided into obligate air breathers and facultative air breathers. Obligate air breathers, such as the African lungfish, must breathe air periodically or they will suffocate. Facultative air breathers, such as the catfish Hypostomus plecostomus, will only breathe air if they need to and will otherwise rely solely on their gills for oxygen if conditions are favourable. Most air breathing fish are not obligate air breathers, as there is an energetic cost in rising to the surface and a fitness cost of being exposed to surface predators.
Fish have a closed circulatory system with a heart that pumps the blood in a single loop throughout the body. The blood goes from the heart to gills, from the gills to the rest of the body, and then back to the heart. In most fish, the heart consists of four parts: the sinus venosus, the atrium, the ventricle, and the bulbus arteriosus. Despite consisting of four parts, the fish heart is still a two-chambered heart. The sinus venosus is a thin-walled sac that collects blood from the fish’s veins before allowing it to flow to the atrium, which is a large muscular chamber. The atrium serves as a one-way compartment for blood to flow into the ventricle. The ventricle is a thick-walled, muscular chamber and it does the actual pumping for the heart. It pumps blood to a large tube called the bulbus arteriosus. At the front end, the bulbus arteriosus connects to a large blood vessel called the aorta, through which blood flows to the fish’s gills.
As with many aquatic animals, most fish release their nitrogenous wastes as ammonia. Some of the wastes diffuse through the gills into the surrounding water. Others are removed by the kidneys, excretory organs that filter wastes from the blood. Kidneys help fishes control the amount of ammonia in their bodies. Saltwater fish tend to lose water because of osmosis. In salt-water fish, the kidneys concentrate wastes and return as much water as possible back to the body. The reverse happens in freshwater fish: they tend to gain water continuously. The kidneys of freshwater fish are specially adapted to pump out large amounts of dilute urine. Some fish have specially adapted kidneys that change their function, allowing them to move from freshwater to salt-water.