Ground-penetrating radar (GPR) is a non-destructive and non-invasive geophysical survey method that has been used to characterize soil volumetric water content (VWC) dynamics. An array antenna GPR system was used to collect nearly seamless, time-lapse multi-offset GPR data during an in-situ infiltration test on sand dunes with limited traces. Because the data volume was significant, an approach was utilized to automatically determine electromagnetic wave velocities from sparse common midpoint (CMP) data using standard velocity analysis, such as semblance analysis. The objective of this study was to develop a methodology that allows one to automatically perform velocity analysis by interpolating sparse CMP data obtained with the array GPR system. The proposed method determined the optimal normal moveout velocity values and the removal range of the F-K zone pass filter that minimized errors between the original and interpolated CMP data using leave-one-out cross-validation (LOOCV). After interpolating the sparse CMP data with the F-K zone pass filter, semblance analysis was used to determine the time-lapse velocity structure of the soil profile during water infiltration. The velocity data were converted to VWC data based on the Topp equation, which relates the soil VWC to the soil dielectric constant. The proposed method was tested using CMP data obtained via numerical simulation and experiments. The VWC profile from the proposed approach matched well with the independently observed VWC profiles obtained from an invasive probe-type soil moisture sensor.