Science is a complex topic and over the past two decades information and communication technologies have had an advantageous impact on science teaching and learning. When information and communication technologies are used into classrooms, students play an active role, learn at school and outside school, improve their teamwork skills, ask more questions, find answers to questions and show a higher interest in learning. The development of pedagogical strategies suited to classroom use of online resources should be an important priority for the science education community. Although many studies have demonstrated the effectiveness of computer-based instruction in the students’ achievement in science, others suggest that students get lost on the Internet when searching information. However, other works have reported that students have difficulties in regulating their learning when using hypermedia environments. Science educators claim the necessity of attempting to facilitate students’ learning of science topics by using scaffolds, or instructional aids, designed to develop appropriate web searching and managerial strategies and to support students’ web-based learning. In response to this educational necessity, our work offers more insight into the challenge of combining information and communication technology with Inquiry WebBased Learning and procedural guidance in order to increase the students’ involvement and responsibility for their own learning of complex science topics. The main goal of the present study is to integrate technology and inquiry into science classrooms to assist students build their own knowledge and answer meaningful driving questions. 27 secondary education students. Specific scaffolds were provided to guide students through complex tasks, to help them develop scientific knowledge, and to provide support to enable them to transfer what they learnt during the web-based activity. All activities were designed keeping in mind the WebQuest structure but also including the circular notion of inquiry process presented by Lim (2004). According to Lim (2004) an inquiry process has the following elements: Ask, Plan, Know, Explore, Construct, and Reflect. Quantitative assessments showed that students in the experimental group outperformed the ones in the control group in the post test, indicating the positive effect of the instructional design. Some clues to use adaptive scaffolds effectively were exposed. Some of these scaffolds are tables, simulators, applets, visualizations, conceptual maps, and note-taking areas/boxes. This research lends evidence to questions regarding the value of students engaging in on-line inquiry learning to enhance science content understanding. The conclusions drawn in this work present a positive and promising path in the design of instructional processes capable to enhance students’ digital literacy and, consequently improve student’s content understanding using web information.