In order to integratedly evaluate the biological safety as a water quality index, an assessment method based on three toxicity tests (algae growth inhibition, daphnia immobilization and larval fish toxicity) was developed. In this study, the developed method was used to screen, evaluate and rank the biological safety of small rivers near agricultural, industrial and residential areas. Twenty-seven representative water samples were collected from the Kaname River watershed and the Hinata River watershed in Kanagawa Prefecture, Japan. The results indicated that (1) the biological safety of water from the Hinata River ranked much higher than those from the Suzu River and the Shibuta River due to less human activities, (2) the biological safety from outlets of paddy fields ranked much worse than those from point source discharges of toxic pollutants, (3) the use of pesticides significantly affected the water quality of nearby small rivers and ditches during the pesticide application season, (4) the effects of different kinds of pesticides could successfully be classified using one toxicity test component of the bioassay battery, and (5) there was no significant quantitative relationship between the toxicity and dissolved organic carbon (DOC) for the studied water samples. The toxicities of water samples in this study were in agreement with the concentrations of pesticides determined with chemical methods by other researchers, which demonstrated that the developed assessment method was reliable to screen site contaminated with organic chemicals for priority management.