In this study, we examined the use of cognitive tools provided in a problem-based hypermedia learning environment for sixth graders. Purposes were to understand how the built-in tools were used, and if tool use was associated with different problem-solving stages. Results showed that tools supporting cognitive processing and sharing cognitive load played a more central role early in the problem-solving process, whereas tools supporting cognitive activities that would be out of students' reach otherwise, and hypothesis generation and testing were used more in the later stages of problem-solving. The findings also indicated that students increasingly used multiple tools in the later stages of their problem-solving process. The various tools, performing different functions, appeared to enable students to coordinate multiple cognitive skills in a seamless way and, therefore, facilitated their information processing. Results also suggested that students with higher performance scores made more productive use of tools than students with lower performance scores. Findings of the study are discussed.