In-channel stream restoration structures readjust surface water hydraulics, streambed pressure, and subsurface hyporheic exchange characteristics. In this study, we conducted flume experiments (pool-riffle amplitude of 0.03 m and wavelengths of 0.5 m) and computational fluid dynamic (CFD) simulations to quantify how restoration structures impacted hyporheic penetration depth, Dp, and hyporheic vertical discharge rate, Qv. Restoration structures were channel-spanning vanes with subsurface footers placed in the gravel bed at each riffle. Hyporheic vertical discharge rate was estimated by analyzing solute concentration decay data, and maximum hyporheic penetration depth was measured as the interface between hyporheic water and groundwater using dye tracing experiments. The CFD was verified with literature-based flume hydraulic data and with Dp and Qz observations, and the CFD was then used to document how Dp and Qz varied with flume discharge, Q, ranging from 1 to 15 L/s (3E + 03 < Re < 5E + 04). Flume experiments and CFD simulations showed that restoration structures increased Qz and decreased Dp, creating a shallower but higher flux hyporheic zone. Qz had a positive linear relationship with Q, while Dp initially grew as Q increased, but then shrunk when a hydraulic jump with low streambed pressured formed downstream of the structure. The restoration structures created counter-acting forces of increased downwelling head due to backwater effects, and increased upwelling due to low streambed pressure and standing waves downstream of the structure.