The purpose of the study was to examine (a) students’ social annotation behaviors and engagement change in an undergraduate course throughout the semester, and (b) which social annotation behaviors impact active engagement time. A total of 91 university students’ social annotation behaviors, as well as their active engagement time in readings, were collected from a social annotation system named Perusall. Longitudinal growth modeling analysis revealed that (a) students’ active engagement time on readings declined over the course of the semester with a significant variation in the changes among individual students, and (b) all social annotation behaviors, except for the number of question upvotes given by students, were positive predictors of active engagement time. These findings are discussed in terms of the implications, limitations, and future directions.