Proper control of water quality is an essential part of any successful aquaculture operation. Immediate test results provided by on-site water analysis equipment can confirm a healthy environment or give early warning signals for required treatment. Even low levels of un-ionized ammonia may affect the fish's central nervous system, reduce its ability to obtain oxygen and lowers resistance to disease. A product of organic waste, ammonia enters the water directly from the fish and from other organic material and uneaten food.
Ammonia levels are pH dependent, and can fluctuate throughout the day.
Different species of fish have different susceptibilities to carbon dioxide toxicity. In some species, excess carbon dioxide hinders the ability of the blood to hold oxygen. Produced during respiration and consumed during photosynthesis, carbon dioxide levels fluctuate throughout the day opposite to dissolved oxygen levels. High carbon dioxide levels lower the pH, which in turn affects the ratio of un-ionized to ionized ammonia. In systems with existing or chronic high nitrite levels, chloride will often be added to prevent the fish from succumbing to nitrite toxicity.