Social annotation plays a crucial role in nurturing and sustaining a collaborative reading community, offering the potential to enhance students’ motivation and performance within socially supportive learning environments. Nonetheless, research on the dynamic changes in student engagement in social annotation remains limited. This study aims to unveil the temporal changes in students’ behavioral, cognitive, affective, and social engagement within the context of social annotation. In addition, it examines the disparities in social annotation behaviors between students with different engagement profiles. Using a multivariate time series clustering approach to analyze a dataset comprising 91 undergraduate students interacting with 29 reading materials, this study identified two distinct engagement profiles. Both profiles revealed a decline in behavioral engagement as the number of reading activities increased. However, students’ cognitive, affective, and social engagement levels in social annotation remained relatively stable across these activities. Subsequent analyses showed that students exhibiting a declining engagement profile displayed higher levels of aggregated behavioral, cognitive, and social engagement. Furthermore, they posted a significantly greater number of annotations and responses to peers’ annotations compared to students characterized by a low engagement profile. Potential explanations and pedagogical implications of these findings were discussed.