Online inquiry, use of the Web as an information resource to inquire into science, has become increasingly common in middle schools in recent years. However, prior research has found that middle school students tend to use the Web in a superficial manner. To address the challenges that students face in online inquiry, we designed the Digital IdeaKeeper, a scaffolded software tool to help students engage in online inquiry through support for inquiry planning, information search, analysis, and synthesis. This study examined the differences between regular and IdeaKeeper-supported online inquiry performed by 8 pairs of sixth graders in naturalistic classroom settings. Analysis of 80 screen videos of students' computer activities and conversations found that IdeaKeeper-supported online inquiry was more integrated, efficient, continuous, metacognitive, and focused. This study has important implications for designing online learning environments for middle school students. (Contains 6 figures and 7 tables.)