The study explored how to best use scaffolds for supporting students' inquiry practices in computer-supported learning environments. We designed a series of inquiry units assisted with three versions of written inquiry prompts (generic and context-specific); that is, three scaffold-fading conditions: implicit, explicit, and fading. We then examined how the three scaffold-fading conditions influenced students' conceptual understanding, understanding of scientific inquiry, and inquiry abilities. Three grade-10 classes (N = 105) participated in this study; they were randomly assigned to and taught in the three conditions. Data-collection procedures included a pretest-posttest approach and in-depth observations of the target students. The findings showed that after these inquiry units, all of the students exhibited significant learning gains in conceptual knowledge and performed better inquiry abilities regardless of which condition was used. The explicit and fading conditions were more effective in enhancing students' understanding of scientific inquiry. The fading condition tended to better support the students' development of inquiry abilities and help transfer these abilities to a new setting involving an independent socioscientific task about where to build a dam. The results suggest that fading plays an essential role in enhancing the effectiveness of scaffolds.