This study focused on characterising aquifer systems based on water-level changes observed systematically at 159 paired groundwater monitoring wells throughout Korea. Using spectral analysis, principal component analysis (PCA), and cross-correlation analysis with linear regression, aquifer conditions were identified from the comparison of water-level changes in shallow alluvial and deep bedrock monitoring wells. The spectral analysis could identify the aquifer conditions (i.e., unconfined, semi-confined and confined) of 58.5% of bedrock wells and 42.8% of alluvial wells: 93 and 68 wells out of 159 wells, respectively. Even among the bedrock wells, 50 wells (53.7%) exhibited characteristics of the unconfined condition, implying significant vulnerability of the aquifer to contaminants from the land surface and shallow depths. It appears to be better approach for deep bedrock aquifers than shallow alluvial aquifers. However, significant portions of the water-level changes remained unclear for categorising aquifer conditions due to disturbances in data continuity. For different aquifer conditions, PCA could show typical pattern and factor scores of principal components. Principal component 1 due to wet-and-dry seasonal changes and water-level response time was dominant covering about 55% of total variances of each aquifer conditions, implying the usefulness of supplementary method of aquifer characterisation. Cross-correlation and time-lag analysis in the water-level responses to precipitations clearly show how the water levels in shallow and deep wells correspond in time scale. No significant differences in time-lags was found between shallow and deep wells. However, clear time-lags were found to be increasing from unconfined to confined conditions: from 1.47 to 2.75 days and from 1.78 to 2.75 days for both shallow alluvial and deep bedrock wells, respectively. In combination of various statistical methods, three types of water-level fluctuation patterns were identified from the water-level pairs: Type I of identical aquifer systems (77.8%), Type II of the different aquifer systems with different recharge flow paths (9.5%), and Type III of unmatched aquifer system pairs and correlations (12.7%). Type I and II could be used as verification of aquifer condition in the paired monitoring system. However, Type III shows the complexity of water-level fluctuation in different aquifer conditions. This study showed that confined or not-confined conditions are not directly related to the depth of wells in the aquifer. Therefore, the utilisation of groundwater as a water-supply source should be carefully designed, tested for its hydrogeologic conditions, and managed to ensure sustainable quantity and quality.