All organisms play important roles in food chain. Any adverse effects on constituents of food chain may cause ecological imbalance. JPRI has developed a battery of bioassays to evaluate acute toxicities and chronic effects using representative species in aquatic environment such as fish, mysid shrimp, water flea, green algae and bacteria. Histological and genetic techniques such as DNA microarray have also been employed for further investigation on long-term effects on aquatic organisms. Research outcomes using these technologies have received a high reputation among academic society. We have investigated cause and effect of pulp and paper mill effluents using the bioassays combined with chemical analyses, resulting in dramatic improvement of effluent quality.