The recent research has shown the bloom toxic of cyanobateria in Sesan River which is one of the largest tributaries of Mekong River. The bloom toxic of cyanobacteria released cyanotoxin which is the serious problem causing adverse health effects for the local people along the river since this river is the main source for daily use. Therefore, the condition growth of cyanobacteria and sources of contamination were investigated after this research which was conducted twice in rainy and dry season. 3 sampling sites along the river that were chosen to be analyzed and monitored the water quality after the occurrence of bloom of the cyanobacteria. The condition growth of cyanobacteria was conducive in term of temperature, pH, and nutrient in rainy and dry season. Data showed the concentration of Phosphate in which range from 0.05mg/l to 0.87mg/l and Nitrate range from 0.75mg/l to 1.53mg/l indicated that the river has been contaminated and it has been the best nutritional condition for its growth and bloom. Additionally, sources of contamination were shown as a result of untreated sewage, agriculture activities, fertilizer, soil erosion, material decay, mining activities and dam construction in the upstream.