This study investigates the added value of stable water isotopes in constraining ecohydrological flux partitioning within the Bétérou basin, a 10,000 km² tropical savanna watershed in northern Benin. It leverages a unique five-year record of high-frequency isotope measurements in river water at the outlet and in precipitation. Using the tracer-enabled, distributed model EcH<sub>2</sub>O-iso, we evaluated how different calibration datasets influence the representation of internal flux partitioning, in particular runoff generation from surface and subsurface pathways, in a region where evapotranspiration (ET) dominates the water budget. A multi-objective calibration was performed across four scenarios, ranging from a baseline using only outlet discharge to a comprehensive setup incorporating intra-basin discharge and isotopic tracers. Our results demonstrate that isotopic tracers are essential for realistically reproducing internal flow partitioning. The inclusion of isotopes drove the model to mobilise older groundwater reservoirs, leading to increased simulated water ages and the dampening of stream isotopic signals. Scenarios calibrated solely on outlet discharge showed high fit for the hydrograph but simulated minimal subsurface contribution, contrary to field evidence from instrumented catchments. Isotopes provided only indirect constraints on ET, whose influence on water partitioning was governed primarily by root water uptake as modulated by land cover. These findings suggest that monitoring strategies in tropical environments where data are often scarce and monitoring priorities must be carefully weighed, should consider the inclusion of isotopic tracers alongside traditional hydrometric observations, as these constrain models to reproduce hydrological functioning for the right reasons and thus provide a more reliable basis for assessing water resources and climate change vulnerability.