<p>A stable and reliable water supply is fundamental to sustainable regional development. Therefore, understanding the contribution of baseflow to water availability during low-flow periods is critically important. Most baseflow separation studies focus on large basins, resulting in a limited understanding of baseflow variability in geologically heterogeneous mountain sub-basins. Using the Nanmoku watershed as a case study, we examined major ions, ²²²Rn, and stable water isotopes (δ¹⁸O and&#xa0;δD) across sub-basins with contrasting geological settings. We used these tracers to elucidate stream-water chemistry and to evaluate tracer-based baseflow separation in small catchments. HCO₃⁻, Ca²⁺, and Mg²⁺ increased in summer, likely owing to enhanced biologically driven weathering, whereas NO₃⁻ was influenced by flushing of soil water. These seasonal effects make these ions unsuitable as tracers for baseflow separation. In contrast, Cl⁻ is the most broadly applicable tracer because it showed a consistent inverse relationship with discharge. Na⁺ may also be useful as a tracer in areas underlain by strata with low abundances of Na-bearing minerals. In sub-basins with low ion concentrations, Cl⁻ is not suitable for baseflow separation; however, elevated ²²²Rn concentrations and reduced variability in δ¹⁸O and δD of stream water indicate a groundwater-dominated, baseflow-like contribution to streamflow. These findings offer a framework for selecting tracers and evaluating baseflow contributions in geologically complex hilly and mountainous catchments.</p>