In this paper, we present two studies designed to help students navigate effectively and learn from a hypertext system, CoMPASS. Our first study (N=74) involved an analysis of students' navigation patterns to group them into clusters, using a k-means clustering technique. Based on this analysis, navigation patterns were grouped into four clusters, enabling us to understand the kinds of support that students needed. This formed the basis of our next study, in which we designed and implemented metanavigation support to help students navigate and learn science content. Support in the form of prompts was provided to one group (N=58) while a second group (N=58) with no support served as the comparison group. Our results suggest that students in the support group performed better on a concept-mapping task. Based on the results we provide suggestions for providing metacognitive support in hypertext systems.Current design-based and project-based approaches to enhance science learning (Krajcik et al., 1991;Kolodner, 1997) emphasize the importance of helping students understand cause and effect relationships among scientific phenomena, use of data to support explanations and opportunities for sustained inquiry in which students investigate questions of their own. While the hands-on activities in an inquiry approach can help students experience scientific phenomena and the relationships therein, electronic texts in the form of hypertext and hypermedia systems (e.g., Shapiro, 2000;Azevedo & Cromley, 2004) as well as digital libraries (e.g., Abbas et al., 2002;Hoffman et al., 2003) are also increasingly being used in scientific inquiry. Digital or hypertext documents are nonlinear and flexible, and enable students to follow their own investigation paths.The flexibility and non-linearity of hypertext systems, attributes that seem to hold great promise, also present challenges for learners and designers. On one hand, hypertext systems present material in different ways allowing the learner to view the same material from