Thinking in and understanding of three-dimensional structures is omnipresent in many sciences from chemistry to geosciences. Current visualizations, however, are still using two-dimensional media such as maps or three-dimensional representations accessible through two-dimensional interfaces (e.g., desktop computers). The emergence of immersive virtual reality environments, both accessible and of high-quality, allows for creating embodied and interactive experiences that permit for rethinking learning environments and provide access to three-dimensional information through three-dimensional interfaces. However, there is a shortage of empirical studies on immersive learning environments. In response to this shortcoming, this study examines the role of immersive VR (iVR) in improving students' learning experience and performance in terms of penetrative thinking in a critical 3D task in geosciences education: drawing cross-sections. We developed a pilot study where students were asked to draw cross-sections of the depth and geometry of earthquakes at two subduction zones after visualizing the earthquake locations either in iVR or 2D maps on a computer. The results of our study show that iVR creates a better learning experience; students reported significantly higher scores in terms of Spatial Situation Model and there is anecdotal evidence in favor of higher reflective thinking in iVR. In terms of learning performance, we did not find a significant difference in the graded exercise of drawing cross-sections. However, iVR seems to have a positive effect on understanding the geometry of earthquake locations in a complex tectonic environment such as Japan. Our results, therefore, add to the growing body of literature that draws a more nuanced picture of the benefits of immersive learning environments calling for larger scale and in-depth studies.