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Field measurements of hydrologic tracers indicate varying magnitudes of geochemical separation between subsurface pore waters. The potential for conventional soil physics alone to explain isotopic differences between preferential flow and tightly-bound water remains unclear. Here, we explore physical drivers of isotopic separations using 650 different model configurations of soil, climate, and mobile/immobile soil-water domain characteristics, without confounding fractionation or plant uptake effects. We find simulations with coarser soils and less precipitation led to reduced separation between pore spaces and drainage. Amplified separations are found with larger immobile domains and, to a lesser extent, higher mobile-immobile transfer rates. Nonetheless, isotopic separations remained small (<4‰ for δ²H) across simulations, indicating that contrasting transport dynamics generate limited geochemical differences. Therefore, conventional soil physics alone are unlikely to explain large ecohydrological separations observed elsewhere, and further efforts aimed at reducing methodological artifacts, refining understanding of fractionation processes, and investigating new physiochemical mechanisms are needed.