A shallow low-lying coastal sand aquifer in southern Finland is vulnerable to the climate change and human activities. Under future climate change, a rise in sea-level would cause some parts of the aquifer and the water intake well to be under seawater. This, together with the predicted increase in precipitation, would enhance groundwater recharge and raise the water table, consequently contributing to the potential deterioration of groundwater quality or potential flooding in the low-lying aquifer area. An information on geological and hydrogeological characteristics of the aquifer for the climate change adaptation plan including the possible new locations of water intake wells was needed. This study aimed to construct a three-dimensional geological model and evaluate heterogeneity of the aquifer to provide a geological framework for groundwater flow model and the assessment of groundwater vulnerability. The methods used consist of a stochastic-geostatistical approach incorporated with groundwater flow model to predict the distributions of the superficial layers of a heterogeneous aquifer and to identify the distributions of the aquifer medias (sand and gravel) as well as groundwater flow system. In addition, the LiDAR-based digital elevation model was utilized to define the flood prone areas under the climate change scenarios. The three-dimensional geological model provides a better characterization of the heterogeneity of the aquifer and improved reliability of subsequent groundwater flow model and vulnerability assessment in the aquifer area. The proposed new locations of water intake wells and the results of the study provided useful information for local authorities for groundwater management in future.