The incorporation of various textual resources into scientific inquiry is important for establishing background knowledge. Many of these resources are now presented in hypertext or hypermedia environments, which require students to comprehend and actively integrate information from multiple sources. Further, numerous practices employed by readers with good comprehension skills align with the practices necessary to successfully conduct scientific inquiry. This paper investigated the relationship between reading comprehension ability for traditional text and navigation behaviors in a hypertext environment within the context of an inquiry-based physics curriculum. Changes in navigation behaviors throughout the curriculum were also examined. Findings indicated that the relationship between reading comprehension ability for traditional text and hypertext comprehension is yet unclear. Study 1 showed no significant relationship between reading comprehension scores on a standardized test and goal-focused hypertext navigation behaviors. In contrast, Study 2 showed that higher comprehension ability students tended to use navigation and comprehension strategies more often and that this pattern also held true for strategy use at the end of the curriculum. Both studies showed that only some goal-focused navigation behaviors increased significantly throughout the unit. Implications for learning with hypertext and hypermedia environments, particularly in the context of inquiry-based science classrooms, are discussed. (Contains 4 figures and 5 tables.)