Understanding the intermittent hydraulic connectivity between ephemeral streams and alluvial aquifers is a key challenge for managing water resources in arid environments. The lower Rio Grande flows for short, discontinuous periods during the irrigation season through the Mesilla Basin in southeastern New Mexico and southwestern Texas. Hydraulic connections between the Rio Grande and the Rio Grande alluvial aquifer in the Mesilla Basin vary spatially and temporally and are not well understood. Self-potential (SP) monitoring and time-lapse electric resistivity tomography (ERT) were therefore performed along linear cross-sections spanning the riverbed and flood plain for more than 4 months to monitor the transient hydraulic connection between the river and the alluvial aquifer by measuring time-lapse changes in the electric potential field in the riverbed and flood plain. The monitoring period began on 21 May 2022, when the riverbed was completely dry, continued through the irrigation season while streamflow was provided by reservoir releases from upstream dams, and ended on 4 October 2022, when the riverbed was again dry. SP monitoring data show (1) a background condition in the dry riverbed consisting of (a) a positive electric potential anomaly with a maximum amplitude of about +100 mV attributed predominantly to a subsurface vertical salt concentration gradient and (b) diurnal electric potential fluctuations with amplitudes of 40,000–90,000 mV attributed to near-surface heat conduction driven by weather variability, in addition to (2) a streaming potential anomaly during the irrigation season with a maximum amplitude of about −3500 mV whose transient behavior clearly exhibited a change from the background anomaly to depict exclusively losing streamflow conditions that persisted through the irrigation season. Time-lapse ERT monitoring results depict rapid infiltration of streamflow into the subsurface and imply the river and Rio Grande alluvial aquifer established a full hydraulic connection within a few hours after streamflow arrival at the monitoring site. SP monitoring data show an apparent transition from hydraulic connection to disconnection at the end of the irrigation season and indicate that the transitional phase between connection and disconnection may last substantially longer than the transition from disconnection to connection. The combination of SP and ERT monitoring demonstrated herein shows the potential for broader applications of time-lapse monitoring of hydraulic intermittency and near-surface heat fluxes in different rivers.