Full-waveform inversion of GPR data has shown a high potential in many applications to obtain accurate and quantitative high resolution images of the subsurface. We implemented a new full-waveform inversion that combines an accurate 3D forward modeling approach with a shuffled complex evolution method that incorporates the complicated wave interactions and interferences that cannot be resolved by standard processes. This new approach is applied to zero-offset profile GPR data that were acquired in horizontal boreholes to monitor soil water content and water uptake by roots under different soil and treatment conditions. Using standard ray-based processing methods, the determined permittivity values close to the surface were not reliable due to interferences from the critically refracted air wave and the direct wave through the subsurface. Synthetic studies showed that traces at depths 0.1 m and 0.2 m are affected by these interferences and hence no reliable permittivity values and soil water content values can be obtain by standard ray-based approaches. The new full-waveform inversion was used to obtain reliable permittivity and soil water content results for three different treatment plots and six different depth positions between 0.06-1.16m of the horizontal boreholes. The inverted results show a good fit with the observed data and quantitative permittivity results were obtained for all depths.