Training undergraduate students in hydrogeology is challenging as students grapple with complex content in a three-dimensional, unobservable, subsurface space. In a prior study with novice to expert hydrogeologists, we found that two spatial thinking skills (visual penetrative ability and working with multiple frames of reference) predicted performance on a contaminated site characterization task. Our current work involves observing and interviewing student groups in introductory hydrogeology courses to see how they use the spatial thinking skills we previously identified. We video recorded nine groups of hydrogeology students as they completed the contaminated site characterization task, which involved constructing a cross-section, contouring a potentiometric surface, completing a three-point problem, and contouring a contaminant plume. We created manipulatives for students to use as they shared their thinking and demonstrated spatial relationships related to the site, the subsurface, groundwater flow, and the contaminant plume. We coded the interviews for student struggle — both spatial and conceptual — as well as for how students resolved their confusion. Common struggles included conflating topography with hydraulic head, conflating topography with contaminant concentrations, conceptual difficulty with confining units, conceptual difficulty with the nature of the potentiometric surface, procedural challenges with drawing contours, and integrating multiple two-dimensional maps into a coherent three-dimensional mental model. Students addressed these challenges with heuristics, by using learned procedures, by relying on naïve mental models, and through peer conversations that helped them grapple with the spatially complex content. In many instances, discourse between peers was especially helpful, particularly when a peer used gestures and manipulatives to demonstrate spatial relationships. This line of inquiry has proven especially fruitful for understanding how students make sense of spatially complex content in hydrogeology and may provide useful insight for hydrogeology instructors who want to better support student learning.