This study is aimed to understand the hydraulic mechanism of coastal aquifer systems that include highly permeable layers (HPLs). These hydrologic conditions can be found in many volcanic islands that are composed of a series of lava flows discharged into sea or other standing body of water. In the first part, we developed a numerical model based on the geologic and hydrologic data obtained from the eastern Jeju Island, Korea, of which the aquifer contains clinker and hyaloclastite layers. The simulation results reproduced spatial location of fresh-saline water interface, especially the abrupt decline of interface at the inland part and the thickness variation of transition zone along the cross-section observed at the eastern Jeju coastal aquifer. We were able to find out that these phenomena are strongly related to the presence of the HPL. In the second part, quantitative analyses were conducted with the use of hypothetical models in order to understand the dynamic characteristics of coastal system that includes HPLs. A series of sensitivity studies were conducted to assess the effect of the horizontal length and vertical depth of HPL on the spatial location of the interface toe and the configuration of transition zone. Various case studies have shown that the seawater intruded into the inland more as the horizontal length of HPL was increased and its vertical depth was decreased. In other simulations including two HPLs, the vertical distance between these two HPLs primarily controlled the flow regime, flux variations, and the configuration of the transition zone. Finally, we performed simulations to evaluate the effect of a rising sea-level. This study provides more understanding of how the presence of HPL controls the seawater intrusion processes, and the spatial configurations of fresh-saline water interface at coastal aquifers. Copyright © 2012 John Wiley & Sons, Ltd.