Technological innovations and changing learning environments are influencing student engagement more than ever before. These changing learning environments are affecting the constructs of student behavioural engagement in the online environment and require scrutiny to determine how to facilitate better student learning outcomes. Specifically, recent literature is lacking in providing insights into how students engage and interact with online content in the self-regulated environment, considering the absence of direct teacher support. This paper investigates how instructional design, informed by the factors relating to behavioural engagement, can influence the student-content interaction process within the fabric of inquiry-based learning activities. Two online learning modules on introductory science topics were developed to facilitate students' independent study in an asynchronous online environment. The study revealed that students showed a high commitment to engaging and completing the tasks that required less manipulative and pro-active effort during the learning process. The findings also revealed that instructional guidance significantly improved the behavioural engagement for student groups with prior learning experience in science simulations and technology skills. This study highlights several issues concerning student engagement in a self-regulated online learning environment and offers possible suggestions for improvement. The findings might contribute to informing the practice of teachers and educators in developing online science modules applicable to inquiry-based learning.