The groundwater quality through livestock excreta survey based on “Act of the management and use of livestock excreta” was investigated by selecting sampling sites within 1 km of the farmland without considering hydrogeological units. However, these sites can be affected by various pollution sources such as chemical fertilizers and livestock excretions. Additionally, the effects of pollution sources on groundwater quality in the sites cannot be clearly distinguished from naturally occurring backgrounds. In this study, a method was developed to select the sampling sites for groundwater quality through livestock excreta survey in order to understand the effects of pollution sources especially livestock excreta. First, the concentrations of nitrate within the radius of 200 m, 300 m, 500 m and 750 m, respectively, from the farms regarded as pollution sources in hydrogeological units were compared in 2016-2017. All the nitrate concentrations at 200 - 500 m from the farms exceeded a background concentration, 13.3 mg/L. Those at 750 m and the background concentrations measured by the Ministry of Environment were comparable. Therefore, the appropriate radius was suggested as 500 m for livestock excretions survey. In this study, the areas within 500 m from the farms could be considered under the influence of livestock excretions, while those beyond 500 from the pollution sources as background in hydrogeological units. The developed method was validated by applying it to the sites selected based on both administrative divisions and watersheds for livestock excretion survey. The average densities for the developed method were 0.82 and 0.39 points/km2, respectively, which were considered as appropriate levels according to those of the European Environmental Agency.