In this paper, we analysed the effect of trench-hill soil surface on ground-penetrating radar (GPR) full-wave inversion for soil moisture measurement. We conducted numerical experiments by modelling the trench-hill surface using finite-difference time–domain (FDTD) simulations. The FDTD simulations were carried out with the open-source software gprMax, using different centre frequencies, namely, 150 MHz, 250 MHz and 450 MHz. The gprMax source/receiver for each centre frequency was calibrated, respectively, to transform the FDTD radar signal to normalized Green’s functions for wave propagation in multilayered media. The radar signals and inversion results of the three different frequency ranges are compared. The FDTD Green’s functions of the trench-hill surface with a flat surface are also compared. The results show that the trench-hill surface only slightly affects the inversion when frequency is lower than 190 MHz, which agrees with Rayleigh’s criterion. Field measurements were performed as well, using a prototype radar mounted on an irrigation robot. The low-frequency antenna was calibrated over a large water plane. The optimal operating frequency range was set to 130–190 MHz. TDR measurements were performed as well for comparison. The results demonstrated promising perspectives for automated and real-time determination of the root–zone soil moisture in potato fields, and thereby for precise and automatic irrigation.