Drilling for groundwater is expensive and challenging. It is even more challenging to find a location that will result in a high-yield well in heterogeneous environments. To tackle the heterogeneity issue, geophysical surveys can help in mapping the subsurface structure and delineating the drilling trajectory. The current study displays the effectiveness of 3D electrical resistivity tomography (ERT) to locate a permeable groundwater zone within a highly heterogeneous and clayey subsurface. Ground truthing the acquired geophysical data with in-situ sampling helps ensure accuracy in classifying groundwater zones in the final inverted 3D data set while also delineating boundaries between permeable groundwater zones and less permeable clayey structures. In-situ samples of groundwater and soil were used to measure the saturated region's resistivity in the laboratory using a column setup. Clay zones in the data set are classified from the nearby well data at similar depth ranges and from very low resistivity values from ERT data and laboratory measurements. The results display highly differentiating resistivity zones that are attributed to the scattered clay lenses (low resistivity) in conjunction with the freshwater zone (high resistivity). The distinction between clayey and nonclayey bodies is important to better inform drilling locations for optimal groundwater yield. This study concludes that with the aid of low-cost geophysical surveys and minimal in-situ sampling data correlations, permeable groundwater boundaries and clay lens volumes can be identified easily.