Aims: Torque teno virus (TTV) is a human DNA virus chronically infecting most healthy individuals worldwide and can be transmitted by faecal-oral route. The occurrence of TTV was evaluated in the streams crossing the city of Manaus (Brazilian Amazon) over a 1-year period, four times a year. Methods and Results: Fifty-two water samples were collected from 13 different locations. Viruses were concentrated from two litres of water by adsorption to negative membrane filters followed by ultrafiltration. TTV DNA was detected by PCR assays designed to detect all five TTV genomic groups. By conventional PCR, 19/52 (37%) samples were positive. By real-time PCR, TTV DNA could be detected in 48/52 (92%) samples. Viral loads ranged from 1300 to 746 000 genome equivalent per 100 ml of river water. Eleven distinct nucleotide sequences were obtained. Conclusions: Our results show the wide distribution and diversity of TTV among Manaus urban micro basins. Significance and Impact of the Study: The data presented here may contribute to substantiate TTV as a sensitive indicator of human contamination.