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Intermittent rivers and ephemeral streams (IRES) make up the majority of waterways in arid and semi-arid regions. While the physical underpinnings of surface water-groundwater (SW-GW) flow systems are well understood, how ephemerality, hydraulic properties and vegetation interact along IRES is not clear, posing severe challenges to their sustainable management. This study sought to identify the controls for SW-GW-vegetation interactions along IRES. To this end, numerical experiments on a quasi-hypothetical IRES cross-section with an integrated surface-subsurface hydrological model were undertaken. The influence of different degrees of ephemerality on infiltration and riverine transpiration was tested by varying the duration of no-flow periods. The influence of hydraulic conductivity (K), moisture retention capacity, root density, and local rainfall was also explored. Experiments showed that infiltration is controlled by ephemerality and K, with infiltration decreasing rapidly with increasing ephemerality and decreasing K. Transpiration is influenced by a complex interplay between ephemerality, hydraulic properties, and vegetation. While transpiration is strongly controlled by the degree of ephemerality, the capacity of the subsurface to maintain variably saturated conditions can strongly attenuate the effects of ephemerality. A large moisture retention capacity of the subsurface can partly compensate for the reduced infiltration under increasing ephemerality. Transpiration can be as large under ephemeral as under perennial conditions, especially where water table fluctuations exhibit large amplitudes within the zone of high root density. Overall, the results provide important insights into the complex dynamics of IRES and highlight how changes in flow dynamics can have significant impacts beyond instream processes.