Groundwater exploration is an alternative to meet raw water needs because of the increasing water demand and the dwindling surface water availability. Water use continues to increase along with the rate of population growth in the Rote Ndao Regency. Therefore, an initial assessment of the presence of groundwater can be carried out by identifying the groundwater basin area. Batutua is one of the groundwater basin areas occupied by the most population because it is the capital of Rote Ndao Regency. This study aims to identify aquifer systems and flow patterns as the basis for groundwater exploration in the Batutua groundwater basin area. The method used in this groundwater aquifer system study is the Vertical Electrical Sounding (VES) method. The VES method is a geoelectrical method used to investigate the layers of an aquifer by interpreting the current that penetrates the soil using two electrodes and the potential response. Geoelectrical investigations were carried out at 8 points in the Batutua groundwater basin area. The aquifer is found in water-containing coral limestone areas where water flows through fractures as secondary permeability. The groundwater flow direction was obtained by measuring the groundwater levels in 14 dug wells and 24 springs. The research’s area aquifer system is formed by upper shallow aquifer as an unconfined aquifer with a thickness less than 20 m and lower shallow aquifer as a semi-confined aquifer that has clay or marls on upper layer and limestone in below with the flow direction from the East to the West and the North part of the study area.