Abstract: Shrimp farm effluents increase concomitantly the deterioration of the mangrove ecosystem, as well as the production in farming itself. The long-term effects of this pollution cause to the growth of the undesirable algaes (Cyanobacteria). The use of the probiotic (Epicin) is the means adopted to fight against these undesirable algaes. The aim of this study was to determine the conditions of efficiency of the probiotic and its effects on the water quality in shrimp farming. The study focus on the water quality parameters of the channel reservoir and thirty ponds. The results showed that with a R²=0,550 and R² adjusted=0,517, the alkalinity and the rate of phosphate from the channel reservoir are the main componment that is the most influency in the growth of Cyanobacterieses in the ponds. High alkalinity is an element that inhibits the efficiency of the probiotics in the struggle against the undesirable algaes. The installation of the bioremediation by these bacteriese causes the reduction of phytoplancton density in the ponds, and also, it decreases the rate of pollutants in the water.