The prevalence of DNA viruses in water from the Tamagawa River, Japan was quantitatively surveyed for 6months, from April to September 2003. A total of 18 river water samples were subjected to virus concentration method using an electronegative membrane, followed by DNA extraction and direct quantitative real-time polymerase chain reaction (qPCR) for DNA viruses. Adenoviruses of serotypes 40 and 41 were detected most frequently in the river water samples tested (61.1%), at a concentration ranging from 3.16×10³ to 1.38×10⁵ copies/l, followed by JC polyomaviruses (11.1%) and torque teno viruses (5.6%). No sample was positive for BK polyomaviruses. In addition, for selective detection of virus particles, adenoviruses 40 and 41 were tested with qPCR combined with an immunomagnetic separation technique; they were detected in only 16.7% of the samples, showing a concentration ranging from 7.42×10² to 4.24×10⁴ copies/l. This study is significant since it is the first study to demonstrate the prevalence of polyomaviruses in water samples in Japan and to use immunomagnetic separation qPCR to detect adenovirus particles in aquatic environments.