An individual’s home range, or how much space it requires to obtain resources and meet its needs for survival and reproduction, affects the scale of many fundamental processes in ecology and can inform the management of species. Although home range size has been described for many taxa in two dimensions (2D), for species that also have a strong vertical component to their movement, such representations can miss core components of their ecology, including the size of their home ranges and the amount of overlap, and thus competition, between individuals. Measuring three-dimensional (3D) home ranges for small-bodied life history stages and species can be particularly difficult, as they cannot tolerate high resolution tracking technologies like GPS collars. In this study, we used Passive Integrated Transponder (PIT) tags to measure the 2D and 3D home ranges of two species of fossorial juvenile salamander: the ringed salamander (Ambystoma annulatum) and the spotted salamander (A. maculatum). We also tested whether individuals modified their habitat selection or movement behavior in response to environmental variation. Salamanders in our study frequently used subterranean habitats. However, we rarely detected them more than 5 cm below ground. Additionally, the overlap among 2D and 3D home ranges, respectively, were similar. These findings indicate that these salamanders may move vertically through their habitat less than previously thought. Alternatively, salamanders may have moved into soil strata beyond the detection range of PIT telemetry. We conclude that PIT telemetry can be a suitable technique for determining the 3D home range of fossorial life-stages or species for which other tracking technologies are unsuitable. When animal behavior includes movements with a vertical component, simplifying assumptions of 2D home ranges can affect ecological inferences by overestimating competition between individuals and underestimating home range size. We used Passive Integrated Transponder (PIT) tags to describe the home range of fossorial juvenile salamanders in 3D. The juvenile salamanders in this study modulated their habitat selection in response to weather, but in general remained close to the soil surface. As a result, juveniles may be more susceptible than previously thought to habitat management practices that alter the local microclimate. Because individuals moved vertically less than predicted, 2D and 3D home ranges had similar patterns. We demonstrate that PIT telemetry can facilitate subterranean tracking of a cryptic life stage. However, this technology is limited in its subterranean detection depth, and until antenna strength is improved, the resolution of 3D home ranges may be limited.