Carbon dioxide, ammonia, nitrite, and hydrogen sulfide are the common toxic metabolites in shrimp ponds. Carbon dioxide is produced through respiration by all aerobic microorganisms, plants, and animals. Ammonia is an excretory product of shrimp. It also is produced during microbial decay of organic matter. Nitrite and hydrogen sulfide are produced by microorganisms when dissolved oxygen concentration is low. Toxic metabolite concentrations increase at higher stocking and feeding rates. Thus, there are seldom problems with toxic metabolites in extensive and semi-intensive shrimp culture (Boyd & Fast, 1992).

Carbon dioxide: Concentrations of carbon dioxide below 20 mg/1 probably are not harmful provided that dissolved oxygen concentrations are sufficient (Boyd & Fast, 1992).

Hydrogen sulfide: This substance is extremely toxic to shrimp. Any detectable concentration probably has adverse effects on growth. The lethal concentration for shrimp is not defined (Boyd & Fast, 1992).

Ammonia: The un-ionized form (NH₃) is most toxic. Concentrations of un-ionized ammonia above 1 mg/1 are potentially lethal; concentrations greater than 0.1 mg/1 may adversely affect growth. At pH 9.0 and salinity 20 ppt, about 25% of total ammonia is un-ionized. Therefore, total ammonia concentrations above 0.4 mg/1 could negatively affect growth when pH is high (Boyd & Fast, 1992).

Nitrite: Nitrite in shrimp ponds is seldom at concentrations great enough to kill shrimp, but growth may be adversely affected by concentrations above 4 or 5 mg/l (Boyd & Fast, 1992).

Nutrients: Inorganic nitrogen compounds (nitrate and ammonium) and phosphate are nutrients that commonly determine phytoplankton abundance. With high feeding rates, there is normally no need to apply these nutrients in fertilizers. In ponds with little or no feeding, fertilizers may be added to encourage phytoplankton growth. Optimum nutrient concentrations are undefined (Boyd & Fast, 1992).

Water analysis kits are adequate for determining concentrations of toxic metabolites. Samples should be collected from near the pond bottom. The sampling time is unimportant, except for carbon dioxide, which should be measured in the early morning. Toxic metabolite concentrations will change quickly during sample storage, so measurements should be made at once or the samples preserved. The best way for preserving samples for a few hours is to place them on ice and in the dark (Boyd & Fast, 1992).

In intensive shrimp ponds, toxic metabolite concentrations can build up over time. Measurements made at one week intervals usually will provide an accurate assessment. Toxic metabolite measurements in extensive or semi-intensive ponds sometimes are needed to explain problems with mortality or slow growth of shrimp (Boyd & Fast, 1992).

Measurements of pH are necessary to interpret ammonia and hydrogen sulfide data. Analytical methods give total concentrations (ionized + un-ionized) of ammonia and sulfide. The proportion of toxic, un-ionized ammonia increases with increasing pH while that of toxic un-ionized hydrogen sulfide decreases with increasing pH (Boyd & Fast, 1992).