The purpose of this study was to elucidate and describe students’ thinking when making connections between substitution and elimination reactions and their corresponding reaction coordinate diagrams. Thirty-six students enrolled in organic chemistry II participated in individual, semi-structured interviews. Three major themes were identified that characterize students’ difficulties with integrating the information from the reactions and the reaction coordinate diagrams: incorrect ideas about the meanings of the reaction coordinate diagrams’ features, errors when examining reaction mechanisms, and an inability to assess the relative energies of reaction species. These findings suggest that students need support for coherence formation between reactions and reaction coordinate diagrams. Implications for teaching to address these student difficulties are suggested.