This study determined the influence of digital literacy and web-based collaborative inquiry learning on the critical and scientific thinking skills of Grade 10 students. It specifically examined students’ level of digital literacy, the changes in thinking skills before and after exposure to scaffolding and case-analysis strategies, the relationship between digital literacy and thinking skills, and the differences between the two approaches. A quasi-experimental research design utilizing the non-equivalent pretest–posttest control group design to determine the influence of Digital Literacy and Web-Based Collaborative Inquiry Learning (WCIL) on the Critical and Scientific Thinking Skills of Grade 10 students. Results showed that students demonstrated high to very high digital literacy across all domains. Significant improvements were observed in critical and scientific thinking skills after the intervention, particularly in problem identification, hypothesis formulation, data interpretation, evaluation and reflection, and creative thinking. However, reasoned decision-making under case analysis did not show a significant difference. A limited but significant relationship was found between selected digital literacy skills and thinking skills, particularly in media analysis and access to information. No significant difference was found between the posttest results of scaffolding and case-analysis groups. The study concludes that integrating digital literacy with inquiry-based learning effectively enhances students’ higher-order thinking skills.