Teachers rely on representations, simulations and animations in their classrooms to explore and expand students’ conceptual understanding in chemistry. Researchers adopt the same visualization tools to investigate student understanding and to support their communication of the outcomes of their research studies. In the past decade, many carefully designed web-based resources including sophisticated simulations and animations have been developed and are accessible online for teachers to engage students in guided and inquiry activities. In spite of decades of research on student difficulties with conceptual understanding, there are few examples of modules incorporating these online resources designed to improve students’ understanding of concepts that underpin learning in tertiary chemistry. In this project, the design and delivery of five online modules covering fundamental chemistry concepts has been explored, informed by research literature in the areas of scaffolding and visual representations. The aim was to encourage students to engage in self-regulated exploration of these modules, initiated by the provision of formative feedback through a diagnostic instrument. Two separate mechanisms for delivering online modules, both integrating existing web-based resources, were trialed and evaluated in terms of student engagement and perceptions.