Many studies have reported the affordances of students' engagement in web-based learning. However, few studies have used a qualitative approach to investigating students' challenges with such type of learning over time. To fill this gap, this study uses the qualitative case study method to explore the challenges of university students with web-based learning in one semester. The data were collected from interviews with and reflections and field notes of students in an English reading class in a university in China. The results revealed limitations in web-based learning due to individual negative factors that evolved incidentally or chronically and due to the interactions between such factors. These factors inhibited student and instructor engagement, including in adjusting to changing circumstances. The study concluded that the challenges of web-based learning in the reading class were multifaceted and constrained the learning process but were mitigated by the efforts of the instructor and the students to overcome the limitations of web-based learning.