Nitrogenous compounds is one of the most important environmental pollution and Ammonia is the most important and dangerous one. Generally in water pollution classification the presence of Nitrite, Nitrate and Ammonia implies that there are inorganic chemical contaminants in the water. In this research the effect of Ammonia acute toxicity on baby Acipenser persicus weighted average of 3 grams in lab situation was studied. The tests were done on 7 cases and 3 repetitions and a whole number of 10 fish by stagnant water method for 96 hours. Fish were exposed to different whole Ammonia concentrations which were 0, 5, 7, 9.5, 13.2, 18 & 25 mg in liter for baby Acipenser persicus. First, the amount of Ammonia LC50 in 24, 48, 72 & 96 hours was gained, this was calculated for baby Acipenser persicus respectively 12.6033, 9.8218, 8.0038, 6.3708 mg in liter whole ammonia. After finding LC50 amounts, we chose one low level of LC50 which is 25% concentration and one high level of LC50 which is 75% concentration and the test was repeated by 4 cases and 3 repetitions. Concentration range for this material was 1.592, 3.185 & 4.778 mg in liter whole Ammonia. Then possible microscopic and Histopathologic lesions of this type of fish's gill, liver and kidney tissue were studied. The results showed that after exposing to Ammonia, some phenomena such as hyperemia, hyperplasia, adhesions secondary lamella, primary lamella swelling, hemorrhage and cell necrosis is observed in the gill, and in the liver some other phenomena such as hyperemia, stagnation of bile, cell necrosis and cell atrophy is observed and finally in the kidney complications like hyperemia, interstitial tissue degeneration, cell necrosis, dilatation of Bowman's space, homosydryn is observed. Generally, the most injuries are observed in these fish's gill.