This study showed the hydrogeological characteristics of an alluvial aquifer that is composed of sand, silt, and clay layers in a small domain. It can be classified into a lower high-salinity layer and an upper freshwater layer and contains shells and remnant paleo-seawater (average 5000 μS/cm) due to sea level fluctuation. Geological and electrical conductivity logging, a long-term pumping test, and multi-depth water quality measurements were conducted at pumping, injection, and observational wells to evaluate the hydrogeologic properties, identify the optimal recharge rate, and assess artificial recharge. Using a hydraulic test, a large difference in drawdown and salinity appeared at the radially located observational wells because of the difference in hydraulic connectivity between the wells in the small study area. It was concluded that the hydraulic anisotropy and heterogeneity of the alluvial aquifer should be carefully examined when locating an injection well and considering the efficient design of artificial recharge.