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Advection through hyporheic zones (HZ) consisting of heterogeneous channel bend streambed deposits and their equivalent homogenous medium was investigated using finite difference groundwater flow and transport simulations and forward particle tracking. The top prescribed head boundary was varied in order to mimic various stream channel head distributions resulting from the presence of bed forms and channel curvature. Flux calculations show that heterogeneity causes significant additional HZ flux compared to an equivalent homogenous medium. However, the major cause of HZ flux is a spatially periodic (sinusoidal) head distribution along the boundary, representing the effect of bed forms. The additional influence of heterogeneity on the total channel-bed exchange and the overall HZ geometry are increased when boundary head sinusoidal fluctuation is more subdued. We present dimensionless numbers that summarize these relationships. Heterogeneity’s influence is further magnified by considering the effect of channel curvature on boundary heads. The simulations illustrate the dynamic influence of heterogeneity on the hyporheic zone since the various head boundaries employed in our modeling efforts are a proxy for different surface water conditions and bed form states that may occur during a single flood. Furthermore, we show that residence times (total tracking times) of particles originating from the streambed follow a lognormal distribution. In the presence of heterogeneity, residence times can decrease or they can increase compared to residence times for homogeneous conditions depending on the relative positions of the heterogeneities and the bed forms. Hence streambed heterogeneity and stream curvature, factors often neglected in previous modeling efforts, combine with bed form configuration to dynamically determine HZ geometry, fluxes, and residence time distributions.