The aim of this study was to investigate whether and how engaging with a computer-supported collaborative knowledge-building environment helps students to develop a more sophisticated approach to scientific inquiry. A total of 52 undergraduate students took a course entitled “Introduction to Natural Sciences” that was based on knowledge-building pedagogy. They were engaged in using the Knowledge Forum (KF) to conduct scientific inquiries and construct scientific concepts through online collaboration. We analyzed (1) the contents of students’ online discussions and (2) students’ online activity logs. Data were subjected to both qualitative and quantitative analysis. The results indicated that (1) after engaging in scientific inquiry using KF, the students were able to develop more sophisticated scientific concepts; and (2) while the quality of the students’ scientific inquiries was overall correlated with the quantity of their online activities, it was found that not all types of knowledge-building activities contribute to effective scientific inquiry. Only when the focus of students’ online activities is placed on sustained idea improvement can the quality of their inquiries actually be enhanced. We discuss possible ways of improving how students conduct online inquiries.