In this study, an interactive process in a Web-based learning environment was planned for the cultivation of students' cooperative learning skills and capacity for scientific inquiry. Based on detailed analyses of students' computer protocols, interview protocols, and test scores, this project sought to analyze the changes in students' scientific concepts and the development of their science process skills (SPS) after they had completed a series of Web-based lessons. Forty senior high school students were chosen and grouped into eight heterogeneous groups for online cooperative learning. As the data showed, the Web-based course used in this study can help students gain a better understanding of subject-related concepts and improve their science process skills. We also found that students with different SPS abilities had significantly different SPS improvement. Low-SPS students have made the most rapid progress in building their science process skills while the high-SPS students made the least progress after interacting with four Web-based lessons. It was also found that heterogeneous grouping in a cooperative learning environment increases the weak learners' motivation and participation.