Within each an AFO type, there are different waste sources, such as manure (feces and urine), animal parts, dead animals, excess feed, feed lot runoff, and others. The species, size and maturity of the animals, as well as the composition of their feed, affect the quantity and characteristics of the manure and other wastes. The four waste categories explicitly regulated by USEPA for facilities designated as CAFOs include manure, litter, process water, and overflow.
The primary pollutants associated with animal wastes (see links below) are nutrients (primarily nitrogen and phosphorus), pathogens, salts, organic matter, solids, and volatile and odorous compounds. To a lesser extent animal wastes are also a source of trace elements, pharmaceuticals (antibiotics and hormones), and pesticides. AFOs may also have waste containing soaps, surfactants, acids, alkalines, and disinfectants used for cleaning, health maintenance, and food safety.