Twenty-eight students (aged 9 to 17) freely explored a science Web site structured either in an outline (linear) format or "puzzle" (non-linear) format for 2.5 hours. Subjects then engaged in tasks involving locational memory and informational recall. The results indicate that presence of metacognitive skills was a necessary but not sufficient condition for learning in hypermedia environments; the navigational structure of the Web site also was important. Metacognitive skill (as measured by the Junior Metacognitive Awareness Inventory (Jr. MAI) (Sperling, Howard, Miller, & Murphy, 2002) and the How I Study Questionnaire (HISP) (Fortunato, Hecht, Tittle, & Alvarez, 1991) was not a significant predictor of measures of retention within an outline structure (where the conventional structure did not stimulate meta-cognitive knowledge), while metacognition was a significant predictor of informational recall within the puzzle structure (which required active meta-cognitive knowledge to make meaning within the unfamiliar structure). The results point to the need for instructional designers to consider the structure of Web sites, with particular emphasis on the use of recognizable conventions, in order to reduce the metacognitive demands upon working memory involved in deciphering the structure.