Previous studies on WebQuest, a pedagogical design to overcome navigational disorientation and information overload, have shown success in directing learners' inquiry on the Internet. Evidences were also found to respectively support critical thinking and reading comprehension through WebQuest reading activities; however, questions still remain as to which aspects of WebQuest activities contribute to their improvements. The present study was intended to advance our understandings of WebQuest-based learning by pointing out specific aspects that improved learners' critical thinking skills. Nine 11th graders from a senior high school in northern Taiwan were recruited to participate in a WebQuest-based English reading program on mobile devices. They joined two cycles of WebQuest reading, with each lasting four weeks. All of their in-class discussions were recorded and transcribed for analyses; and, they turned in their reflection journals and were interviewed after each cycle. When learning with WebQuest alone, our participants developed their critical thinking skills by establishing their criteria for screening information. Later, in their discussions with group members, they refined their critical thinking skills by constant negotiations. The present study attributed the participants' development of critical thinking skills to the presentations of sequenced reading tasks on WebQuest websites and the guided questions embedded in each WebQuest reading task. It also emphasized peer negotiations for sharpening their critical thinking skills.