This study was objected to provide suggestions for best management practices to restore the cultural and historical values of the wells in Palaces as well as their water qualities. Water resources in the five Palaces in Seoul Metropolitan, including Gyeongbokgung, Changdeokgung, Changgyeonggung, Jongmyo Shrine, and Deoksugung, were surveyed for their physical flows and chemical compositions from April to July in 2010. Ground waters in most wells were found at depths within 5 m from the ground surface, showing typical water-table aquifer systems. Hydraulic gradients indicate water resources in Gyeongbokgung, Changdeokgung, and Changgyeonggung flowing toward south, and toward east in Deoksugung area. Especially, water-level fluctuation data at S-10 in Deoksugung implied the influence of groundwater discharge facility. In Jongmyo Shrine, water was not detected in wells, indicating the water level was lower than the well depth. Based on the water chemistry and stable isotope analyses, water resources and their qualities appeared to be formed by the water-rock interaction along the groundwater paths. S-10 (Deoksugung) and S-14 (Changgyeonggung) samples were contaminated with nitrate ($NO_3$) in levels of higher than Korean drinking water standard, 10 mg/L as $NO_3$-N, but once in four sampling campaigns. In the situation that water resources in Palaces still maintain natural characteristics, the materials that will be used for the restoration and improvement of the Palace water supplies should be carefully selected not to disturb the natural integrity. In addition, because the wells are located in the center of metropolitan area, a systematic monitoring should be applied to detect and to manage the potential impacts of underground construction and various pollution sources.