The water quality of environmental waters from the viewpoint of aquatic ecotoxicity was investigated using a three-species ecotoxicity test (algae, daphnia and fish). Water samples were collected, concentrated with a solid-phase extraction technique and exposed to each test species. The growth inhibition, immobilization (swimming inhibition) and mortality ratios in acute toxicity tests for algae, daphnia and fish, respectively, were used as water quality indexes. For the river waters, 38% of the monitoring sites showed good water quality from the viewpoint of long-term ecotoxicity for all the three test species because no toxicity effects were observed at the concentration factors of 10, 50 and 50 for algae, daphnia and fish, respectively. For the agricultural drains, the ecotoxicity level responded sensitively especially when agricultural chemicals were applied. The GC/MS analysis also confirmed that the detection index (DI) in the agricultural drains was often raised significantly by the agricultural chemicals, but the period with high ecotoxicity did not continue for long.