Effluent management systems have long been rationalized based on individual chemical compounds in Japan.However, such systems essentially hold difficult problems for the management of hazardous influences of new chemicals and their mixtures. In the fiscal year of 2009, Ministry of the Environment, Japan has started the discussion on the implementation of whole effluent toxicity systems that have already been popular in USA, Korea and other countries. We have conducted some preliminary bio-assays to examine the effluents from several industries including paper mills in Tokushima prefecture using short-term chronic tests adopted in USA. The short-term chronic bio-assays using three organisms such as fish, daphnia and algae could detect significant toxicity in the effluents with a wide range of spectra with high sensitivity. These results provide information much differing from conventional chemical analysis and are directly related to the protection of ecosystems in the receiving water areas.