Undergraduate students may possess underdeveloped knowledge about water systems, particularly groundwater. The use of models and modeling have been employed in undergraduate classrooms to support students' learning about water. However, effective modeling requires spatial thinking skills, which undergraduate students may need to develop. To address this need, we developed a multi-week intervention involving an array of spatial thinking activities to support undergraduate students' use of a computer-based groundwater modeling tool. This intervention took place in an intro-level undergraduate water course. Students used the model to complete a task involving a groundwater contaminant scenario. Here, we report findings from a comparative study conducted in two consecutive semesters: Year 1 (n=56) and Year 2 (n=46), the latter of which involved the intervention. We explored their understanding of space, representation, and reasoning (NRC, 2006) by conducting quantitative and qualitative analyses on student tasks and interviews. Findings suggest that students in year 2 better articulated concepts of space. However, students in both years did not perform as expected on tools of representation or reasoning. Students exhibited a relatively limited understanding of representation within the model, particularly about contour lines. Students also struggled to reason about groundwater using information from the model. Overall, these results suggest students struggle with certain aspects of spatial thinking in relation to this groundwater modeling tool. These findings have implications for undergraduate teaching and learning about groundwater.