The current study applied a Web-based inquiry-learning environment Young Researcher for science learning. The environment supported students' inquiry processes with scaffolds for enhancing self-regulation and reflection. Empirical results suggest that students' inquiry skills and the quality of students' regulative processes improved in this learning environment. The reflection as a scaffold helped foster students' regulative activities and enhance their capabilities in inquiry activities. It guided students toward significant improvements in formulating research questions and hypotheses, planning study and drawing conclusions, and in increasing the quality of all of their regulative activities--planning, monitoring, and evaluation. In addition, the results showed that all regulative activities correlate with the level of inquiry skills and with each other. Therefore, students' reflection of regulative activities should be supported to achieve higher gains in inquiry learning.