In this study, a water footprint methodology that reflects the characteristics of domestic water resources, was developed and calculated the water footprint for expressway system as an infrastructure. Water footprint characterization factors were developed for groundwater and surface water in six representative watersheds which are Han River Basin, Nakdong River Basin, Geum River Basin, Seomjin River Basin, Youngsan River Basin, and Jejudo. Three different water footprint methodologies, Boulay’s methodology, Korea Ministry of Environment methodology, this study methodology were compared in an actual construction case of expressway. As the results, the water footprint of 1 km and 4 lane expressway with Boulay and MOE methodology showed 58,804 ㎥ H2Oeq, 42,036 ㎥ H2Oeq, respectively throughout whole life cycle. However, 9,478 ㎥ H2Oeq. of water footprint was calculated by using this study methodology. This difference is mainly due to a developed regional characterization factor, and its related water consumption coefficient of the construction materials.