Ammonia is the primary nitrogenous waste produced by fish from protein digestion. Mammals produce urea, which is a complex of ammonia and carbon. Any nitrogenous waste from manure runoff into the pond, inorganic fertilizer, plant decomposition, and/or uneaten feed is transformed into ammonia by bacteria in the pond. Bacteria of the genus Nitrosomonas convert ammonia into nitrite. Both ammonia and nitrite are toxic to fish. The level of ammonia toxicity depends on the species of fish, water temperature, and pH. The level of nitrite toxicity depends on the species of fish and the chloride ion concentration in the pond water. Sublethal levels of ammonia are known to cause gill and tissue damage, poor growth, and increased susceptibility to disease. Nitrite at sublethal levels reduces oxygen transport into the fish, resulting in poor feed conversion, reduced growth, and increased susceptibility to disease.
At stocking densities normally recommended for cage culture, neither ammonia or nitrite toxicity problems should be encountered. In ponds where higher density cage culture is attempted, where livestock manure can wash into the pond during rains, or where a plankton die-off has occurred, the level of ammonia (and laternitrite) may pose problems.