Temperature controls the rate at which food is transformed into energy which then in turn affects breathing, food intake, bodily growth and physiological behavior. An increase in temperature will decrease the dissolved oxygen content in water which will in turn increase the fish metabolic rate and its demand for oxygen. Any organisms or bacteria also in the water will then be competing for the limited supply of dissolved oxygen, hence causing stress, limited growth, and an increase in carbon dioxide.

Dissolved Oxygen (DO) is considered to be the most important water quality parameter in aquaculture. Depending on the size and type of fish farm, DO levels can change very quickly and can therefore endanger the lives of the fish in a matter of minutes or hours. If the DO level falls too low, fish will suffocate. However, if the DO level is too high, energy will be wasted through the aeration of the water.

The recommended pH range for fish and vertebrates is between 7.0 and 8.0 as the average blood pH is around 7.4. Fish become stressed if pH falls outside the pH 5-10 range. pH does vary throughout the day and depends on the oxygen demand in the water and photosynthesis. CO2 is also released overnight, hence lowering pH by morning but rises to its peak in the afternoon when CO2 consumption by algae (photosynthesis) is at its peak.

Ammonia is the main waste product produced by fish and is regarded as the second most important water quality parameter after dissolved oxygen in intensive fish farming. Even in relatively small concentrations, ammonia can cause significant stress and damage to fish, especially bacteriological infections. In higher concentrations where the nitrogen cycle is not in balance, ammonia can wipe out whole fish stocks.