Research has shown the potential of a problem-based approach to enhance students' learning. The interactive nature of hypermedia technology and its ability to deliver information in different media formats can provide unique capabilities for implementing problem-based learning (PBL) environments. Yet, we know little about the types of tools that are effective in supporting students' learning in a hypermedia supported PBL environment. The purpose of this study was to investigate both the use of tools and design features in a piece of PBL software and their effectiveness on middle school students' learning. The findings of this study show that students who were exposed to the PBL environment increased their achievement scores from pre to posttest more than those students who learned the same content in the traditional classroom. Students' reading ability was found to be a better predictor for their achievement in PBL than their math ability. However, the brief treatment of the study had only limited impact on students' attitude toward learning science. The findings of the study and their implications are discussed in detail.