AbstractHeterogeneity in hydraulic conductivity (K) and channel morphology both control surface water‐groundwater exchange (hyporheic exchange), which influences stream ecosystem processes and biogeochemical cycles. Here we show that heterogeneity in K is the dominant control on exchange rates, residence times, and patterns in hyporheic zones with abrupt lithologic contrasts. We simulated hyporheic exchange in a representative low‐gradient stream with 300 different bimodal K fields composed of sand and silt. Simulations span five sets of sand‐silt ratios and two sets of low and high K contrasts (1 and 3 orders of magnitude). Heterogeneity can increase interfacial flux by an order of magnitude relative to homogeneous cases, drastically changes the shape of residence time distributions, and tends to decrease median residence times. The positioning of highly permeable sand bodies controls patterns of interfacial flux and flow paths. These results are remarkably different from previous studies of smooth, continuous K fields that indicate only moderate effects on hyporheic exchange. Our results also show that hyporheic residence times are least predictable when sand body connectivity is low. As sand body connectivity increases, the expected residence time distribution (ensemble average for a given sand‐silt ratio) remains approximately constant, but the uncertainty around the expectation decreases. Including strong heterogeneity in hyporheic models is imperative for understanding hyporheic fluxes and solute transport. In streams with strongly heterogeneous sediments, characterizing lithologic structure is more critical for predicting hyporheic exchange metrics than characterizing channel morphology.