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Abstract The fate of nutrients and contaminants in fluvial ecosystems is strongly affected by the mixing dynamics between surface water and groundwater within the hyporheic zone, depending on the combination of the sediment's hydraulic heterogeneity and dune morphology. This study examines the effects of hydraulic conductivity stratification on steady‐state, two‐dimensional, hyporheic flows and solute residence time distribution. First, we derive an integral transform‐based semi‐analytical solution for the flow field, capable of accounting for the effects of any functional shape of the vertically varying hydraulic conductivity. The solution considers the uneven distribution of pressure at the water‐sediment interface (i.e., the pumping process) dictated by the presence of dune morphology. We then simulate solute transport using particle tracking. Our modeling framework is validated against numerical and tracer data from flume experiments and used to explore the implication of hydraulic conductivity stratification on the statistics andpdfof the residence time. Finally, reduced‐order models are used to enlighten the dependence of key residence time statistics on the parameters characterizing the hydraulic conductivity stratification.