• Time-lapse electrical resistivity before, during, and after the intermittent river flooding. • Resistivity used to characterize the transient and spatial connectivity transitions. • Resistivity changes due to water saturation characterized connectivity transitions. • Resistivity changes after connection occurred were dominated by river temperature. • Resistivity sensitivity to temperature was also used to characterized infiltration. In the current era of rapid environmental changes, more rivers are projected to dry up and transition to disconnected systems in unprecedented duration and frequency. However, river-groundwater interactions, including connectivity, remain a challenge to characterize, especially for managed-ephemeral rivers such as the lower Rio Grande in southern New Mexico, where conjunctive use for irrigated agriculture is prevalent. This investigation used a noninvasive and spatially distributed geophysical method for mapping the disconnection/connection of groundwater with the Rio Grande River, which has been validated with ancillary data that includes river flow, water levels in the river and adjacent wells, and river and groundwater temperature and electrical conductivity. Time-lapse monitoring of electrical resistivity before, during, and after the river flooding season was used to characterize the transient and spatial connectivity of the water table with the Rio Grande, from disconnection to connection, and back to disconnection. The relationships between electrical conductivity from the geophysical analysis versus the large array of ancillary data helped to narrow down the driver of observed temporal changes in connectivity after the transition from disconnection to connection. The results convey that water temperature is potentially the main influence on the changing electrical conductivity after the connectivity transition. The surface water temperature showed a direct and strong correlation to the electrical conductivity of shallow sediments, which was similar to the river stage/groundwater elevation drivers of infiltration. Time-lapse electrical resistivity can be used to monitor river-groundwater connectivity throughout the intermittency cycle, due to its sensitivity to changes in both water saturation and temperature.