We developed a new tracer-aided hydrological model that disaggregates cockpit karst terrain into the two dominant landscape units of hillslopes and depressions (with fast and slow flow systems). The new model was calibrated by using high temporal resolution hydrometric and isotope data in the outflow of Chenqi catchment in Guizhou Province of south-western China. The model could track hourly water and isotope fluxes through each landscape unit and estimate the associated storage and water age dynamics. From the model results we inferred that the fast flow reservoir in the depression had the smallest water storage and the slow flow reservoir the largest, with the hillslope intermediate. The estimated mean ages of water draining the hillslope unit, and the fast and slow flow reservoirs during the study period, were 137, 326 and 493 days, respectively. Distinct seasonal variability in hydroclimatic conditions and associated water storage dynamics (captured by the model) were the main drivers of non-stationary hydrological connectivity between the hillslope and depression. During the dry season, slow flow in the depression contributes the largest proportion (78.4%) of flow to the underground stream draining the catchment, resulting in weak hydrological connectivity between the hillslope and depression. During the wet period, with the resulting rapid increase in storage, the hillslope unit contributes the largest proportion (57.5%) of flow to the underground stream due to the strong hydrological connectivity between the hillslope and depression. Meanwhile, the tracer-aided model can be used to identify the sources of uncertainty in the model results. Our analysis showed that the model uncertainty of the hydrological variables in the different units relies on their connectivity with the outlet when the calibration target uses only the outlet information. The model uncertainty was much lower for the "newer" water from the fast flow system in the depression and flow from the hillslope unit during the wet season and higher for "older" water from the slow flow system in the depression. This suggests that to constrain model parameters further, increased high-resolution hydrometric and tracer data on the internal dynamics of systems (e.g. groundwater responses during low flow periods) could be used in calibration.