Knowledge about the stochastic nature of heterogeneity in subsurface hydraulic properties is critical for aquifer characterization and the corresponding prediction of groundwater flow and contaminant transport. Whereas the vertical correlation structure of the heterogeneity is often well constrained by borehole information, the lateral correlation structure is generally unknown because the spacing between boreholes is too large to allow for its meaningful inference. There is, however, evidence to suggest that information on the lateral correlation structure may be extracted from the correlation statistics of the subsurface reflectivity structure imaged by surface‐based ground‐penetrating radar measurements. To date, case studies involving this approach have been limited to 2D profiles acquired at a single antenna centre frequency in areas with limited complementary information. As a result, the practical reliability of this methodology has been difficult to assess. Here, we extend previous work to 3D and consider reflection ground‐penetrating radar data acquired using two antenna centre frequencies at the extensively explored and well‐constrained Boise Hydrogeophysical Research Site. We find that the results obtained using the two ground‐penetrating radar frequencies are consistent with each other, as well as with information from a number of other studies at the Boise Hydrogeophysical Research Site. In addition, contrary to previous 2D work, our results indicate that the surface‐based reflection ground‐penetrating radar data are not only sensitive to the aspect ratio of the underlying heterogeneity, but also, albeit to a lesser extent, to the so‐called Hurst number, which is a key parameter characterizing the local variability of the fine‐scale structure.