It is shown the possibility of using the model reaction with cholinesterase inhibition for qualitative and quantitative determination of Cyanobacteria toxic metabolites in natural waters and algae cells. It was established that changes of cultural medium pH may be registered by spectrophotometric method with using of bromine thymol blue indicator or by electrometric method with indexes of pH-meter. Depending on degree of cholinesterase inhibition the different quantity of organic acid is evolved. It is determined that method differs from other biochemical methods by rapidity and may be used under field conditions.