This paper presents an alternative method for monitoring groundwater levels and estimating specific yields of an unconfined aquifer under different seasonal conditions. The approach employs the Time-Lapse Electrical Resistivity Imaging (TL-ERI) method and machine learning-based time series clustering. A TL-ERI survey was conducted at ten sites (WS01-WS10 sites) throughout the dry and wet seasons, with five-time measurements collected for each site, in the Taichung-Nantou Basin along the Wu River, Central Taiwan. The obtained resistivity raw data was inverted and converted into normalized water content values using Archie’s law, followed by applying the Van Genuchten (VG) model for the Soil Water Characteristic Curve to estimate the Groundwater Level (GWL), and estimated the theoretical specific yield (Sy) by computing the difference between the saturated and residual water contents of the fitted VG model. In addition, the specific yield capacity (Sc), representing the nature of the storage capacity in the aquifer, was also calculated. The results showed that this approach was able to estimate those hydrogeological parameters. The spatial distribution of the GWL reveals that during the dry-wet seasons from February to July, there was a high GWL that extended from southeast to northwest. Conversely, during the wet-dry seasons from July to October, the high GWL shrank, which can be attributed to recharge variations from rainfall events. The determined spatial distribution of Sy and Sc fall within the range of 0.03–0.24 and 0.14–0.25, respectively. To quantitatively establish areas of similar groundwater level changes along with the VG model parameter variations during the study period, a Time series Clustering analysis (TSC) was performed by utilizing Hierarchical Agglomerative Clustering (HAC). The findings suggest that the WS03 site is a promising area for further investigation due to its highest Sc value with a slight change in groundwater levels during the dry and wet seasons. This study brings an advanced development of the geoelectrical method to estimate regional hydrogeological parameters in an area with limited available groundwater observation wells, in different seasonal conditions for groundwater management purposes.