ABSTRACT Hyporheic exchange has been shown to provide essential ecosystem functions such as biogeochemical opportunities for nutrient processing. Hyporheic exchange flux (HEF) and residence time (RT) in the hyporheic zone are highly influenced by the size of instream morphological structures ranging from ripples to bars. In this study, the hyporheic flow induced by different geometries of gravel mid‐channel bars (MCB) was simulated numerically using a Computational Fluid Dynamics (CFD) Model. For validating the numerical results, experiments were conducted for ellipse geometry MCBs in the laboratory. The results demonstrated that non‐dimensional exchange flux (q*) and vertical penetration depth of hyporheic path lines (d H *) decreased from partially to fully submerged flow conditions. Moreover, q* increased when the bar height increased for fully submerged flow conditions and by increasing bar length, q* was increased for partially submerged conditions. Outcomes also revealed that the nondimensional median resident time (MRT*) decreases by increasing both the height and length of the bar for fully submerged conditions. Dimensionless hyporheic characteristics obtained from the simulations displayed good correlations with dimensionless geometry and hydraulic characteristics. This research established an important foundation for exploring the biogeochemical dynamics occurring within the hyporheic zone.