Aquifers are generally composed of highly permeable layers that can conduct a considerable amount of groundwater. Traditionally, aquifer units are correlated through the concept of lithostratigraphy. For low-permeable aquifers, it is difficult to define the spatial distribution of hydrogeological units, and this study attempts to use geochemical modeling to identify the groundwater flow paths in an area of Taiwan. Multiple geochemical analyses, including groundwater chemistry; stable isotopic compositions of hydrogen, oxygen and carbon; and radiocarbon contents were performed. Using these parameters as the constraints of geochemical models, the hydraulic connection was examined between pairs of possibly interlinked wells along four selected cross sections, and the conceptual groundwater model was accordingly established. The resultant model suggests that the hydraulic connection between aquifers should be correlated with the concept of chronological stratigraphy, especially for low-permeable, unconsolidated aquifers. Using Darcy’s law, the hydraulic conductivities of the fine-sand aquifers were estimated to be between 3.14 × 10−5 and 1.80 × 10−4 m/s, which are roughly one order of magnitude higher than those derived by in situ pumping tests. The substantial extraction of groundwater over a long period in the studied area could accelerate groundwater flow, leading to an overestimation of the aquifer permeability.