With increased chemical and economic development activities in upstream areas, the amounts of pollutants released have increased, and as such, so has the need for positive management of water supply source areas. Although more than 90% of the water supply sources in Korea depend on direct intake from surface water, the interest in indirect intake, such as riverbank filtration water, has recently risen, with some local governments currently undertaking indirect intake. Even in cases of indirect intake, water supply source protection zones need to be assigned for the comprehensive control of pollutants. To establish water quality protection zones for indirect intake, the scope of the protection zones needed to reflect the hydrological features of the water-bearing deposits of each site. Water source protection areas were estimated and presented as the 1st (within a 100 m radius from an intake well) and 2nd (within a 2 km radius from an intake well) zones. The 1st zone was more sensitive; hence, the installation of various facilities should be prohibited, and the area should be regarded as off-limits. For the 2nd zone, appropriate management should prohibit and restrict activities already present in the water source protection zone.