This study examined how background knowledge, scientific reasoning ability, and various scaffolding forms influenced students' science knowledge and scientific inquiry achievements. The students participated in an online scientific inquiry program involving such activities as generating scientific questions and drawing evidence-based conclusions, while being scaffolded either directly or indirectly. Results indicated that student knowledge and scientific reasoning can predict scientific inquiry ability development. Only scientific reasoning has a significant effect on student comprehension. Level of scientific reasoning and types of scaffolding significantly influenced students' scientific inquiry abilities. In particular, prior reasoning skills significantly affected how they identified variables and made conclusions in both post- and retention tests. Students who used the online program benefitted from direct scaffolding, which helped them make hypotheses and draw conclusions better than indirect scaffolding. Direct scaffolding was especially useful for students with high prior reasoning skills. Students with high prior reason skills who used direct scaffolding were better able to make hypotheses and draw conclusions.