One of the most important environmental problems of Miankaleh wetland in recent years was high mortality of wild waterbirds occurrence in 2020. The present study was conducted to perform a comprehensive monitoring of this event and accurate diagnosis of the cause of death, due to the environmental significance of wild waterbirds mortality, through standard passive Surveillance methods and clinical, autopsy and laboratory studies. The estimated death of birds was 38587, during 50 days. The highest losses were related to Common Coot (about 85%) and flamingos (6%). 198 birds were sampled from different species of birds in two areas (Behshahr and Galuogah). Tissue samples included samples of pharyngeal and tracheal swabs, cloaca, whole blood and blood serum of live birds, and brain, tracheal, lung, gizzard and anterior gastric tissues, intestines and its contents, liver, spleen, pancreas and Chest muscle of dead birds. Tests performed on the samples included: influenza serotypes, Newcastle disease, avian Cholera, pasteurella, duck viral enteritis, duck viral hepatitis, differential diagnosis between gram-negative and gram-positive bacteria, presence of mercury, Arsenic and the remnants of pesticides in tissues and samples, cyanide in water. All tests were negative, except for botulin toxin. According to the results, Clostridium botulinum poisoning is cause of high casualties of waterfowl in Miankaleh Wetland. Laboratory results were shown that the physicochemical properties of alluvium and water create favorable conditions for the production of biotoxins and if it will be not managed, they may recur in the coming years.