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. Plain Language Summary Intermittent rivers and ephemeral streams (IRES) make up the majority of waterways in arid and semi‐arid regions. While the physics of surface water‐groundwater (SW‐GW) 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 key mechanisms which control SW‐GW‐vegetation interactions along IRES through simulation experiments undertaken with a state‐of‐the‐art flow model. Simulation results revealed that infiltration of stream water is controlled by the degree of ephemerality and the hydraulic conductivity of the subsurface, with infiltration decreasing rapidly with an increase in ephemerality and decrease in hydraulic conductivity. Transpiration is influenced by a complex interplay between ephemerality, hydraulic properties and vegetation. The capacity of the subsurface to retain soil moisture can strongly attenuate the effects of ephemerality such that riverine transpiration may be as large under ephemeral as under perennial flow conditions, provided that 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. Key Points Key controls for SW‐GW‐vegetation interactions along ephemeral streams were identified with integrated hydrological models Streambed infiltration is controlled by ephemerality and hydraulic conductivity (K) and is largest under perennial streams Transpiration is controlled by ephemerality, K, soil moisture and root density and can be as large in ephemeral as in perennial systems