The goal of this study was to investigate the effect of two different cooperative learning approaches, namely, the Jigsaw Cooperative Approach (JCA) and the Traditional Cooperative Approach (TCA), on students' learning and practices/actions within the context of a WebQuest science investigation. Another goal of this study was to identify possible problems that students face within the context of a WebQuest when following either approach and to provide suggestions for developing web-based learning tools that enable students to overcome these problems. The sample of the study consisted of 38 seventh-graders, who, according to their science teachers, had prior experience with TCA and JCA. All participants studied about the ecology, architecture, energy and insulation of CO2-friendly houses through the use of a WebQuest science investigation. The data collection involved conceptual tests, screen-video captured data and interviews. Results revealed no differences between the two approaches, in terms of enhancing students' understanding of concepts related to CO2-friendly houses, because of (a) JCA students' inability to apply one of the JCA components, namely, teaching one another about learning material they solely studied, and (b) the fact that the JCA students started applying the TCA after failing teaching one another in the context of JCA. Finally, a number of problems that students faced within the context of a WebQuest science investigation when following the JCA or TCA were identified.