This is a terminal research project that investigates the effects of the Bukidnon Sugar Company in Pulangui River based on the water quality parameters, phytoplankton counts, effects on caged tilapia and toxicity test over a period of three years. Tests show that the natural high flow rate of the river contributes an important factor in diluting the pollutants and controlling the phytoplankton population. Sugar mill waste water caused the death of tilapia. Fish and the invertebrate species and some phytoplankton genera are enumerated.