Biological wastes range from human and animal wastes, to compost and other plant material, to pathogenic microorganisms. Sources include homes, animal laboratories, hospitals, farms, paper mills, and food manufacturing industries.

Acute ground-water quality and human health problems have been recorded from rural areas in all parts of the world where domestic water supplies are taken from surface streams, shallow wells or boreholes situated adjacent to farmyards. Such water is commonly contaminated by animal or human faecal bacteria. Slurry from livestock farms can contain Cryptosporidium, a potentially deadly parasite that can not be destroyed by fast filtration or chlorination of water supply. The extremely high BOD (biological oxygen demand) values of silage effluents, together with the organic contaminants resulting from the fermentation, can lead to intense ground-water contamination, including the onset of foetid anoxic conditions

Adequate incineration of hospital wastes and other infectious material is a pressing concern. Swimmers often suffer from infections due to biological pollution of the sea by disposal untreated sewage and beach lifeguards in Cornwall, UK, now routinely need vaccination against hepatitis.