The Vamanapuram experimental catchment has been established in a humid tropical setting, where the hydrological processes are poorly characterized and have received limited attention. The Monthly River water, groundwater, and rainwater samples have been collected from May 2022 to April 2024 to understand the spatial and seasonal variability of baseflow contributions. The Chemical (Electrical conductivity, silicate) and isotopic tracers (δ 18O, δ 2H) have been used to estimate the baseflow contribution (and associated uncertainty) and the mean transit time of river water. The two-component Classical Hydrograph Separation (CHS, mass balance-based) and the recent Ensemble Hydrograph Separation (EHS, correlation-based) have been used to quantify baseflow contributions. Although CHS and EHS resulted in almost similar baseflow contributions, but EHS is recommended due to reduced uncertainty. Estimated baseflow contributions using EC as a tracer are significantly lower than those estimated using other tracers. Estimates based on silicate, δ 18O, and δ 2H are also generally comparable, and isotopic tracers have a higher degree of uncertainty in estimates than chemical tracers, silica can be used as alternate tracer for baseflow estimation. The baseflow is found to be dominant contributor to streamflow (irrespective of season and location) with fraction greater than 0.5. Mean transit time of stream water ranges between 45 and 143 days, mainly controlled by topography (mean watershed elevation and slope). The groundwater wells found to be behave differently, indicating either seasonal replenishment by rainfall, or steady state or lack of replenishment and diminishing potential of wells. The Trend analysis of groundwater stable isotopic data, and levels indicated that parts of catchment are not getting replenished by rainfall, and groundwater resources are at risk, and needs immediate urgent attention.