Several bodies of surface water in Korea were surveyed for the presence of hepatitis A virus (HAV) between 2007 and 2010. Of 265 surface water samples, 9 (3.4%) were HAV-positive. HAVs were mainly detected in the summer (3/62, 4.8%) and spring (4/96, 4.2%) seasons. Comparing different water sources, the highest prevalence (6.6%) of positive samples was seen in lake water, four HAV-positive samples being from lakes. Comparing prevalence rates across the four representative Korean basin systems, no HAVs were found in the Han or Nakdong river basins. The highest HAV prevalence was found in samples from the Yeongsan river and other basins (6.3%); the Geum/Seom river was also found to have a high HAV prevalence (5.7%). HAVs from the nine positive samples were then sequenced and analyzed phylogenetically. Two of the HAVs belong to genotype IA and fall within the same cluster as HAVs 6-3(ASAN4) (EU049548), KANSAN-PS1 (EU049554), and ASAN-KM (EU049563), which were collected from the stools of patients with gastroenteritis in Korea. The seven other HAV nucleotide sequences belong to the genotype IB cluster. This is the first nationwide surveillance of HAV in major Korean water sources.