Solute transport in interconnected rivers and hyporheic zones is typically modeled through dual-domain models where first-order solute mass transfer between the two domains, ΩR and ΩHZ, is represented by a coefficient α. The transient storage model (TSM) is an example of such an approach. In practice, α is determined by fitting the tails of solute tracer breakthrough curves using a TSM. This approach has led to ambiguity regarding α’s physical meaning and transferability. Here, we investigated the physical basis for α and tested it with virtual experiments through the fully coupled multiphysics model hyporheicFoam for the ΩR−ΩHZ system. hyporheicFoam explicitly simulated coupled flow and solute transport over a kilometer with centimeter-scale resolution. Model results were analyzed to calculate α following its theoretical definition directly. Using the determined α within a TSM enables accurate reproduction of solute transport, underscoring α’s physical relevance and precision.