High-resolution shallow seismic reflection experiments were conducted during and after a pumping test of an agricultural irrigation well to image the cone of depression. Although variations in the reflection time from the top of the saturated zone were not observed, amplitude-versus-offset (AVO) analysis revealed changes in reflection amplitude responses that correlate temporally and spatially to expected changes to the partially saturated zone induced by the pumping and recovery of the aquifer. The AVO responses exhibit dependence on aquifer drawdown and recovery cycles and the distance from the pumping well. We propose that near-surface soil heterogeneity and relatively rapid changes in the water table elevation during irrigation cycles caused a thickening of the partially saturated zone above the water table, which resulted in detectable changes in seismic reflection amplitudes. This study offers insights about the response of shallow seismic reflections to changes in subsurface water saturation and the potential application of seismic techniques to hydrogeophysical problems.