Antibiotics are used extensively in medicine, livestock raising and aqua culture. The spread of antibiotic resistant bacteria from hospitals and livestock farms into the environment has become a public health concern. The information on the occurrence of resistant bacteria in water bodies, however, is very scarce. In this study, about 40 E. coli strains were isolated from river waters collected in the Kaname, Tama and Tsurumi Rivers. The Kaname River receives a large amount of agricultural effluent, while the Tama and Tsurumi Rivers contain a large percentage of sewage treatment plant effluent. Antibiotic resistance patterns were determined by detecting resistance against nine types of antibiotic. The pattern of the Kaname River water was different from those of Tsurumi and Tama River waters. E. coli strains isolated from the Kaname River were determined to originate from livestock feces, and E. coli strains isolated from the Tsurumi and Tama Rivers were of human origin.