To improve the understanding of flow and transport processes in the critical zone, high-resolution and accurate estimation of the small-scale heterogeneity is essential. Preferential flow paths related to high-porosity layers and clay lenses in gravel aquifers greatly affect flow and transport processes in the subsurface, and their high electrical contrast to their surrounding matrix and limited extent can act as low-velocity electromagnetic waveguides. In the past decade, time-domain full-waveform inversion (FWI) of crosshole ground-penetrating radar (GPR) data has shown to provide 2D decimeter-scale resolution images of relative permittivity and electrical conductivity of the subsurface, which can be related to porosity and soil texture. Most studies using crosshole GPR FWI resolved high-porosity zones that were identified by an amplitude analysis approach. But clay lenses or zones with higher electrical conductivity that act as low-velocity waveguides are hard to distinguish in the measured data and amplitude analysis because of the absence of characteristic wave-propagation features. We have investigated a set of nine crosshole GPR data sets from a test site in Hermalle-sous-Argenteau near the Meuse River in Belgium to characterize the aquifer within a decimeter-scale resolution and to improve the understanding of a previously performed heat tracer experiment. Thereby, we extend the amplitude analysis to identify two different types of low-velocity waveguides either caused by an increased porosity or a higher electrical conductivity (and higher porosity). Combining the GPR amplitude analysis for low-velocity waveguide zones with the standard FWI results provided information on waveguide zones, which modified the starting models and further improved the FWI results. Moreover, an updated effective source wavelet is estimated based on the updated permittivity starting models. In comparison with the traditional FWI results, the updated FWI results present smaller gradient of the medium properties and smaller root-mean-squared error values in the final inversion results. The nine crosshole sections are used to generate a 3D image of the aquifer and allowed a detailed analysis of the porosity distribution along the different sections. Consistent structures of the permittivity and electrical conductivity show the robustness of the updated FWI results. The aquifer structures obtained by the FWI results agree with those results of the heat tracer experiment.