Waterborne viruses infect the human population through the consumption of contaminated drinking water and by direct contact with polluted surface water during recreational activity. Although water related viral outbreaks are a major public health concern, virus detection is not a part of the water quality monitoring scheme, mainly due to the absence of routine analysis methods. In the present study, we implemented various approaches for water concentration and virus detection, and tested on Hungarian surface water samples. Eighty samples were collected from 16 sites in Hungary. Samples were concentrated by glass wool and membrane filtration. Human adenoviruses were detected by conventional and quantitative real-time polymerase chain reaction (PCR) methods in 56% (45/80) of the samples; viral titers ranged from 8.60 × 101 to 3.91 × 104 genome copies per liter. Noroviruses and enteroviruses were detected in 30% (24/80) and 13% (10/80) of samples, respectively, by reverse transcription-PCR assays. Results indicate a high prevalence of viral human pathogens in surface waters, suggesting the necessity of a detailed survey focusing on the quality of natural bathing waters and drinking water sources.