The fluxes between groundwater and surface water play a significant role in quantifying water balance along stream reaches to continent scales. Changes in these dynamics are occurring due to aquifer depletion, where pre-development baseflow conditions have transitioned to losing conditions. This problem is studied along the Arkansas River in Western Kansas across a stream reach that transitions from near steady state to losing conditions, and contributes focused recharge to a depleting Ogallala Aquifer. Existing hydrologic data illustrates the lack of understanding they provide related to the control of fluxes exerted by alluvial deposits. Electrical resistivity imaging (ERI) surveys were conducted along this river transect to elucidate the dynamic hydrologic connection existing between the Arkansas River and underlying Arkansas Alluvial and Ogallala Aquifers. Temporal changes in ERI profiles are associated with the transient hydrologic conditions below the water-sediment interface, and complement the hydrogeologic interpretations of the individual ERI profiles. Additionally, fine grained soil inclusions may become revealed by temporal changes in resistivity due to differences in their water holding capacity relative to that of a surrounding matrix of coarser grained soil across changes in recharge. These findings corroborate the role of river-aquifer connectivity and riverbed heterogeneity on localized recharge through embedded assemblages of fine and coarse grained soils.