Monitoring groundwater-surface water (GW-SW) interactions is essential for effectively managing the available water resources in semi-arid and arid environments. The focus of this study was to quantify how much SW is being exchanged with the shallow GW aquifer in the Treasure Valley (TV), Idaho, USA. Previous water budgets estimated regional canal seepage without incorporating canal variability and flow measurement uncertainty. To address this, we applied both direct (gain/loss) and indirect (electrical resistivity tomography (ERT)) techniques. Direct seepage measurements were taken on canals capturing a range of different characteristics in the TV. The discrete measurements were then used to estimate the total seepage anticipated to be lost from these canals during the irrigation season. Our findings showed high seepage variability across the canals. The ERT inversion approach was utilized before and after the irrigation season by applying an advanced inversion scheme to better constrain the canal seepage spatial variability and uncertainty by quantifying changes in the saturated zone with 2D-ERT results. Temporal changes in the subsurface resistivity were observed due to the lateral flow from the nearby surface canal during the irrigation season. The combination of these approaches improves our understanding of SW-GW interactions in intensively managed irrigation systems.