This study reports the impacts of the Scientific Concept Construction and Reconstruction (SCCR) digital learning system on eighth grade students' concept construction, conceptual change, and scientific reasoning involving the topic of "atoms". A two-factorial experimental design was carried out to investigate the effects of the approach of instruction and students' level of scientific reasoning on their pre-, post-, and retention-Atomic Achievement Test, Atomic Dependent Reasoning Test, and Scientific Reasoning Test. The control group (N=100) received conventional instruction whereas the experimental group (N=111) received an SCCR Web-based course. Results indicate that the experimental group significantly outperformed the conventional group on post- and retention-Atomic Achievement Test and Atomic Dependent Reasoning Test scores, and retention-Scientific Reasoning Test scores. Moreover, students with a higher level of scientific reasoning significantly performed better than students with a lower level of scientific reasoning, regardless of their scores on post- and retention-Atomic Achievement Test and Atomic Dependent Reasoning Test. This study successfully demonstrates that the experimental group students outperformed the conventional group students in the domains of concept construction, conceptual change and scientific reasoning. Moreover, students with a higher level of scientific reasoning were more able to successfully change their alternative conceptions. (Contains 3 figures and 4 tables.)