Excess nitrogen and phosphorus may leach to groundwater and contaminate surface water in runoff and erosion. Nitrate pollution can cause disease in humans and livestock. Phosphorus, while not directly toxic to humans or livestock, can cause eutrophication (fertilization of surface waters by nutrients not previously there). Eutrophication leads to algae production and pond scum, which interferes with the use of water for fisheries, recreation, industry, agriculture and drinking. The resulting oxygen depletion and toxin production can also be harmful to the health of humans, livestock, wildlife and fish.

Bacteria (e.g. E. coli, Salmonella), protozoa (e.g. Cryptosporidia, Giardia), and pesticide contamination of water may be harmful to the health of humans and livestock.