The hydraulic properties of aquitards are not easily obtained because monitoring wells are usually installed in aquifers for groundwater resources management. Earthquake-induced crust stress (strain) triggers groundwater level variations over a short period of time in a large area. These groundwater anomalies can be used to investigate aquifer systems. This study uses a poroelastic model to fit the postseismic variations of groundwater level triggered by the Chi-Chi earthquake to evaluate the hydraulic properties of aquitards in the Jhoushuei River alluvial fan (JRAF), Taiwan. Six of the adopted eight wells with depths of 70 to 130 m showed good agreement with the recovery theory. The mean hydraulic conductivities (K) of the aquifers for the eight wells are 1.62 × 10-4 to 9.06 × 10-4 m/s, and the thicknesses are 18.8 to 46.1 m. The thicknesses of the aquitards are 11.3 to 42.0 m. Under the isotropic assumption for K, the estimated values of K for the aquitards are 3.0 × 10-8 to 2.1 × 10-6 m/s, corresponding to a silty medium. The results match the values obtained for the geological material of the drilling core and those reported in previous studies. The estimated values were combined with those given in previous studies to determine the distribution of K in the first two aquitards in the JRAF. The distribution patterns of the aquitards reflect the sedimentary environments and fit the geological material. The proposed technique can be used to evaluate the K value of aquitards using inverse methods. The inversion results can be used in hydrogeological analyses, contaminant modeling, and subsidence evaluation.