With the proliferation of technology, electronic texts in the form of hypertext and hypermedia systems as well as digital libraries are increasingly being used in scientific inquiry. Digital or hypertext documents are nonlinear and flexible, and enable students to follow their own investigation paths. However, the flexibility also poses challenges for students as it pushes students to make decisions as they selectively browse through the space. The research described in this paper aimed to understand (1) how providing students with a visual representation that mirrors the conceptual structure of the domain affects navigation and learning and (2) whether continued use of a hypertext system enables students to learn from it regardless of its structure. (Contains 8 figures, 3 tables and 2 notes.)