Success in chemistry requires not only the ability to recruit prior knowledge but also the ability to establish strong connections between new and existing concepts to form knowledge clusters around core principles. How these knowledge structures are organized can be used to understand the relationships between concepts within a student’s mind. 618 undergraduate students in a general chemistry course participated in this study at a US institution. The purpose of this study was to determine the effect, if any, that prior knowledge in chemistry and mathematics and gender have on the formation of students’ knowledge structures. In addition, the structures were analyzed to identify the hidden connections between macroscopic, submicroscopic, and symbolic representations of chemical knowledge. To visualize these structures, a word association test (WAT) was created to determine concept relatedness. Student response data was then transformed into a series of distances by a computer program called JPathfinder, which created visual representations of the knowledge structures in the Gephi platform. The meaning and implications of these structures were discussed to provide ideas for teaching interventions that focus on weakly associated basic general chemistry concepts. The potential uses of WAT were also shared to help educators identify student misconceptions.