Spatial thinking is essential for nurturing spatially literate graduates in tertiary education. However, there is limited research on individual differences in cognitive processes and their impact on spatial problem solving in disciplinary contexts. This study aimed to investigate cognitive processes involved in spatial thinking in geography majors using a web-based geographic information systems (GIS) mapping tool. The results revealed three clusters characterised by distinctive cognitive processes: "spatial analytic," "spatial diagrammatic" and "alternative." Each cluster adopted unique spatial strategies to solve problems with web-based GIS. Notably, "spatial analytic" learners demonstrated the most optimal profile, resulting in high spatial task performance. These findings have implications for maximising students' learning potential in spatial thinking in the tertiary classroom, optimising performance outcomes in spatial problem solving and building intelligent tutoring systems for adaptive learning.