A method is described for the joint use of time-lapse ground-penetrating radar (GPR) travel times and hydrological data to estimate field-scale soil hydraulic parameters. We build upon previous work to take advantage of a wide range of cross-borehole GPR data acquisition configurations and to accommodate uncertainty in the petrophysical function, which relates soil porosity and water saturation to the effective dielectric constant. We first test the inversion methodology using synthetic examples of water injection in the vadose zone. Realistic errors in the petrophysical function result in substantial errors in soil hydraulic parameter estimates, but such errors are minimized through simultaneous estimation of petrophysical parameters. In some cases the use of a simplified GPR simulator causes systematic errors in calculated travel times; simultaneous estimation of a single correction parameter sufficiently reduces the impact of these errors. We also apply the method to the U.S. Department of Energy (DOE) Hanford site in Washington, where time-lapse GPR and neutron probe (NP) data sets were collected during an infiltration experiment. We find that inclusion of GPR data in the inversion procedure allows for improved predictions of water content, compared to predictions made using NP data alone. These examples demonstrate that the complimentary information contained in geophysical and hydrological data can be successfully extracted in a joint inversion approach. Moreover, since the generation of tomograms is not required, the amount of GPR data required for analyses is relatively low, and difficulties inherent to tomography methods are alleviated. Finally, the approach provides a means to capture the properties and system state of heterogeneous soil, both of which are crucial for assessing and predicting subsurface flow and contaminant transport.