Residents living in karst area barely find clean water resources for their daily needs. Typical karst geological settings which consist of easily dissolved limestone cause groundwater to be accommodated in caves, underground rivers and random subsurface veins. Underground dam could be the best solution for groundwater assessment and management due to its complexity. Its construction captivates and gathers all the water from the various veins then stores it behind the intake wall. The southern part of Okinawa Island is a sea shore area where Ryukyu limestone spreads well. It has many livestock farms as well as numerous agricultural fields growing vegetables and sugarcanes. There was not enough surface water for agricultural and domestic use. To meet those demands, Komesu and Giza Subsurface Dams were established in 2005. The objectives of this study are to determine the environmental effects and the effect of those subsurface dams to the groundwater quality and quantity, using multiple stable isotope analysis (N, C and S isotopes/ CNS-IT). The result showed that Komesu and Giza Subsurface Dams were able to hold the groundwater at one area. Especially during the rainy season, the groundwater level could exceed Komesu’s intake wall (70m) and outflow the underground dam. Nitrate concentration in the groundwater was relatively high, nitrate as nitrogen concentrations were more than 10 mg/L (20 of 69 observation points). Nitrate and sulfate isotopes analysis presented the groundwater was contaminated by chemical fertilizer, with the value of deltas nitrogen-15 mostly around 6-14‰ and deltas sulfur-34 approximately -2 to 5‰. Indeed, the deltas nitrogen-15 versus the deltas sulfur-34 plot proved that autotrophic denitrification happened across the basin. Carbon isotopes traced the major source of the carbon came from terrigenous soil which were planted by C4 plants with value of deltas carbon-13 around -10 to -16‰. Meanwhile, Komesu Underground Dam had also proved that it could block the seawater intrusion. Total dissolved solid value at the outside of the dam was around 1200 and 400-600 inside the construction. The long term monitoring data would be presented before and after the underground dam construction.