Hyporheic exchange influences water quality and controls numerous physical, chemical, and biological processes. Despite its importance, hyporheic exchange and the associated dynamics of solute mixing are often difficult to characterize due to spatial (e.g., sedimentary heterogeneity) and temporal (e.g., river stage fluctuation) variabilities. This study coupled geophysical techniques with physical and chemical sediment analyses to map sedimentary architecture and quantify its influence on hyporheic exchange dynamics within a compound bar deposit in a gravel‐dominated river system in southwestern Ohio. Electromagnetic induction (EMI) was used to quantify variability in electrical conductivity within the compound bar. EMI informed locations of electrode placement for time‐lapse electrical resistivity imaging (ERI) surveys, which were used to examine changes in electrical resistivity driven by hyporheic exchange. Both geophysical methods revealed a zone of high electrical conductivity in the centre of the bar, identified as a fine‐grained cross‐bar channel fill. The zone acts as a baffle to flow, evidenced by stable electrical conditions measured by time‐lapse ERI over the study period. Large changes in electrical resistivity throughout the survey period indicate preferential flowpaths through higher permeability sands and gravels. Grain size analyses confirmed sedimentological interpretations of geophysical data. Loss on ignition and x‐ray fluorescence identified zones with higher organic matter content that are locations for potentially enhanced geochemical activity within the cross‐bar channel fill. Differences in the physical and geochemical characteristics of cross‐bar channel fills play an important role in hyporheic flow dynamics and nutrient processing within riverbed sediments. These findings enhance our understanding of the applications of geophysical methods in mapping riverbed heterogeneity and highlight the importance of accurately representing geomorphologic features and heterogeneity when studying hyporheic exchange processes.