We investigated the epidemiological characteristics of the antimicrobial resistant Enterococcus isolates from the four major rivers of Korea in 2012. A total 316 surface water samples were collected from three distinct sites (nearby livestock farms, tributaries, and major rivers) at two different seasons (dry season: n = 76, wet season: n = 240). A total 654 bacterial cells were isolated from samples and their genus distribution were determined. We found that Gram-negative bacteria including various genera were prevalent (n = 522, 79.8%), and Enterococcus was the most common genus of Gram-positive bacteria (n = 119, 18.2%). The isolation rate of Gram-negative bacteria was higher in wet season, whereas that of Enterococcus isolates was higher in dry season. The prevalence of Enterococcus isolates was also higher nearby livestock farms than on tributaries and main rivers. Since Enterococcus isolate is a key indicator for animal fecal contamination, the following experiments focused on this microorganism. As compared to a previous report in 2006, the resistance rates in E. faecium to erythromycin (40.0% to 69.9%) and chloramphenicol (0% to 16.4%) were increased, whereas those to penicillin (56.0% to 4.1%) and teicoplanin (36.0% to 0%) were decreased. We also found that antimicrobial-resistant (AMR) E. faecium isolates from rivers and livestock samples shared similar pulsed-filed gel electrophoresis (PFGE) profiles, validating the transmission of AMR Enterococcus isolates from livestock to river. Taken together, this study provides us with detailed information about bacterial contamination status in four major rivers, and highlights the changes in AMR pattern of Enterococcus isolates, which are expected to have originated from livestock.