The abundant scientific resources on the Web provide great opportunities for students to expand their science learning, yet easy access to information does not ensure learning. Prior research has found that middle school students tend to read Web‐based scientific resources in a shallow, superficial manner. A software tool was designed to support middle school students in reading online scientific resources through three key strategies: making explicit a skim–read–summarize structure for online reading, using prompts to guide students' reading and foster articulation of thinking, and connecting reading to learning purposes. This study examined the differences between regular and guided online reading performed by eight pairs of sixth graders in a science inquiry project. The students' online reading processes and conversations were captured by a screen‐recording programme. Analysis of 60 h of screen videos showed that the students' online reading in the regular condition was cursory, fragmented, and opportunistic, while the structured online reading was more deliberate, thorough, and purposeful. Overall, the results suggest that middle school students' online reading of scientific resources needs to be guided.