Computer-based learning environments (CBLEs) are effective to the extent that they can adapt to the needs of individual learners by systematically and dynamically providing scaffolding of key learning processes during learning. The ability of these environments ’ to provide adaptive, individualized instruction is derived from an understanding of how learner characteristics, system features, and the mediating learning processes interact within particular contexts. A critical aspect of providing individualized instruction is scaffolding, or instructional support in the form of guides, strategies, and tools which are used during learning to support a level of understanding that would be impossible to attain if students learned on their own. Despite our ability to provide scaffolding concerning well-structured tasks within traditional CBLEs such as intelligent tutoring systems (ITS), providing adaptive scaffolding of students’ learning about conceptually challenging domains, such as the circulatory system and ecology, remains a challenge for hypermedia instruction. We argue that harnessing the full power of hypermedia learning environments will require empirical research aimed at understanding what kinds of scaffolds are effective in facilitating self-regulated learning, and when they are best deployed. Our research therefore focuses on examining the effectiveness of different human