This paper presents a methodology instructors can use in class to elucidate concept understanding in order to design appropriate interventions. The methodology consists of (i) phrasing qualitative questions on fundamental course concepts and (ii) identifying in the answers the main categories that describe the variation of the students' thinking. The application of the methodology is demonstrated for the concept of “soil structure” in an environmental geotechnics course. The results reveal the students' misconceptions related to soil porosity and permeability. To address these misconceptions, alternative in-class activities are discussed.