Interactive features of the hyper-video environment, such as indexing, bookmarks, links to learning materials, multiple-choice questions, and personal and shared annotations, can enhance learning processes. This paper examines integration of the "Annoto" hyper-video platform in three large undergraduate courses (A, B & C) at a large university. The study combines learning analytics of video-recordings of synchronous lessons (9-15 sessions per course, approximately two hours each), content analysis of the hyper-video annotations written by students and lecturers, and semi-structured interviews with the lecturers and with actively-participating students. The log-analysis was conducted at the user level (n = 880) and at the video level (n = 37). Content analysis was based on the Community of Inquiry framework (Garrison et al. in Internet High Educ 2(2):87-105, 1999, Internet High Educ 13(1):5-9, 2010). The findings revealed that when hyper-video is integrated without academic credit, slightly over 10% of undergraduates chose active participation, beyond watching videos and reading others' annotations. The majority of annotations were shared posts and replies (73-96%), rather than personal notes. Relative to the number of students, the rate of reading annotations was significantly higher in Course C. Accordingly, content analysis revealed significantly more "cognitive presence" and "social presence" codes in Course C, while the amount of "teaching presence" was similar in all courses. However, the three courses used the same interaction pattern of annotations: "student's question-lecturer's answer", without promoting peer feedback. The implications for educational theory and the pedagogical design of hyper-video in academia are discussed.