Stable isotopes of water are ideal tracers to integrate into process-based models, advancing ecohydrological understanding. Current tracer-aided ecohydrological modeling is mostly conducted in relatively small-scale catchments, due to limited tracer data availability and often highly damped stream isotope signals in larger catchments (>100 km²). Recent model developments have prioritized better spatial representation, offering new potential for advancing upscaling in tracer-aided modeling. Here, we adapted the fully distributed EcH₂O-iso model to the Selke catchment (456 km², Germany), incorporating monthly sampled isotopes from seven sites between 2012 and 2017. Parameter sensitivity analysis indicated that the information content of isotope data was generally complementary to discharge and more sensitive to runoff partitioning, soil water and energy dynamics. Multi-criteria calibrations revealed that inclusion of isotopes could significantly improve discharge performance during validations and isotope simulations, resulting in more reasonable estimates of the seasonality of stream water ages. However, capturing isotopic signals of highly non-linear near-surface processes remained challenging for the upscaled model, but still allowed for plausible simulation of water ages reflecting non-stationarity in transport and mixing. The detailed modeling also helped unravel spatio-temporally varying patterns of water storage-flux-age interactions and their interplay under severe drought conditions. Embracing the upscaling challenges, this study demonstrated that even coarsely sampled isotope data can be of value in aiding ecohydrological modeling and consequent process representation in larger catchments. The derived innovative insights into ecohydrological functioning at scales commensurate with management decision making, are of particular importance for guiding science-based measures for tackling environmental changes.