Chemistry is traditionally perceived as difficult to comprehend. Its mastery requires that a variety of concepts be linked to form an organized knowledge system. The connections need to be made not only between the concepts associated with the macroscopic level of the chemistry triplet but also between the submicroscopic and symbolic levels. Many factors influence a learner’s success in bridging concepts between these levels. In this study, the aim was to identify and examine the changes in general chemistry students’ knowledge structures by utilizing Word Association Tests. Although many studies have examined knowledge structures and aspects of the chemistry triplet, almost none has considered both at the same time. This study highlights the interconnectedness between the chemistry triplet and changing knowledge structures in overall student populations and in high- and low-achieving students. It provides insights on why students fail to understand chemistry and suggests ideas for future research as limiting factors were noted.