Stable water isotopes are fundamental tracers for interpreting snowpack dynamics, stratigraphy, and meltwater export in the cryosphere. However, the isotopic signals exported from melting snow and ice are often modified internally before release, as natural snowpacks and glacier ice are vertically isotopically heterogeneous and percolating meltwater undergoes dynamic isotopic exchange with the surrounding solid matrix. Here, we quantified how initial isotopic stratigraphy and meltwater flow regimes jointly control this non-conservative isotope transport. We conducted eight controlled column-melting experiments using two-layer ice columns composed of isotopically depleted and enriched layers arranged in reversed vertical sequences under different melting conditions. Effluent &delta;¹⁸O and &delta;²H were interpreted using a process-based, one-dimensional isotope-exchange model. The experiments show that meltwater isotopic evolution is governed primarily by the vertical order of the isotopically distinct layers and cannot be explained by conservative end-member mixing alone. The model successfully reproduced the observed isotope trajectories using effective exchange parameters, yielding exchange rate constants (<em>k_r</em>) of 0.11&ndash;0.54 h^&minus;¹ for oxygen isotopes and 0.11&ndash;0.49 h^&minus;¹ for hydrogen isotopes, with no statistically distinguishable difference between the two isotopic systems within individual experiments. Across the experiments, <em>k_r</em> tended to increase with percolation velocity, most clearly in depleted-top configurations, whereas the active exchange fraction (<em>f</em>) decreased under faster-flow conditions within each stratigraphic group. This hydrodynamic decoupling demonstrates that isotopic exchange during meltwater percolation is dictated not only by contact time but also by flow-path organization and the accessibility of ice-water interfaces. Our results highlight that isotopic signatures exported from melting snow and ice must be interpreted as process-modified signals rather than strictly conservative source end-members. Incorporating flow-dependent phase exchange into cryospheric models will improve the interpretation of meltwater export dynamics and the evolution of isotopic stratigraphy in snow- and ice-dominated environments.