The elimination of baseflow due to declining groundwater levels has compromised many ecological functions of the Cosumnes River. Numerical modeling has shown that floodplain reconnection can be a viable method to increase groundwater recharge - mitigating overdraft and helping re-establish perennial flows in the Cosumnes River. This study investigates the role of subsurface heterogeneity in governing floodplain recharge processes at a proposed managed aquifer recharge site located on the lower Cosumnes River. The spatial arrangement of subsurface materials in alluvial aquifer systems has been shown to control the magnitude, distribution, and temporal dynamics of groundwater surface water interaction. A highly resolved subsurface model of the site was developed to help illuminate areas where we anticipate increased percolation, groundwater perching, and localized stream-aquifer reconnection. Using a nested-scale approach, these results are integrated with regional data from the lower Cosumnes basin to develop a framework for evaluating regional impacts on groundwater levels and flow dynamics.