We consider the transient electrokinetic response of an aquifer-aquitard system to groundwater abstraction from the aquifer. The system was instrumented with 18 non-polarizable copper/copper sulphate electrodes installed at three different depths in the aquitard above the aquifer. The sensing electrodes were installed at depth of 1, 2, and 4 m below ground surface along three overlapping transects. The differential voltages relative to a single permanent electrode were measured with a Campbell Scientific CR1000 datalogger with a single multiplexer. Additionally, six piezometers screened in the top 1.5 m of the confined aquifer, were installed by direct-push. All the piezometers were instrumented with pressure transducers to measure directly the hydraulic response of the aquifer. The vertical variation of resistivity in the aquitard was measured on sediment cores recovered from one of the boreholes used to install the deepest piezometer. The resistivity distribution at antecedent sediment wetness (moisture content) was measured using the MC Miller resistivity boxes and meter, with wetness measured gravimetrically. Previous exploratory drilling and sampling activities at the site indicate that the aquifer is fractured greywacke sandstone overlain with clayey aquitard of semi-consolidated alluvial sediment, with the aquifer-aquitard contact at a depth of 10.3 m below the ground surface. We report the results of the site instrumentation, monitoring, characterization, hydraulic testing, and compare the results of parameter estimation using streaming potential and hydraulic data separately and jointly. We explore the effect of depth of installation of the electrodes in the aquitard on signal strength and quality and compare this to model predicted behavior using semi-analytical models from the literature. The results suggest the need for deep sensing of electrokinetic signals generated by groundwater flow to improve signal-to-noise ratios and the usefulness of self-potential data for hydrogeophysical characterization of aquifer-aquitard systems.