AbstractSatellite laser altimetry reveals short timescale changes in Antarctic ice sheet surface elevation that are suggested to be driven by subglacial water transport and storage. Here details of the interaction between the dynamics of ice stream flow, subglacial water system, and bed elevation relief are examined in the context of idealized, heterogeneous bed geometries. Using a two‐way coupled model of ice and subglacial water flow, we show that basal topography controls the temporal and spatial variability of the sub–ice stream hydraulic system. The orientation and characteristic dimensions of the topographic undulations determine the morphology (connected subglacial ponds or channel‐like subglacial water features) and timescales of the sub–ice stream drainage system. The short‐term (several years to decades) variability of the simulated coupled ice stream/subglacial water system suggests that the short‐term surface variations detected in remote sensing observations may be indicative of a rapidly evolving subglacial water system. Our simulations also show that interaction between ice flow and the highly dynamic subglacial water system has a strong effect on effective stress in the ice. Large effective stress magnitudes arise over areas where the basal traction is characterized by strong spatial gradients, that is, transitions from high to low basal traction or vise versa. These transitions migrate on multiyear timescales and thus cause large effective stress variability on the same temporal scales.