A shared document-based annotation tool was presented, and its usefulness in two different real-life web-based university-level courses (adult learners, n = 27 and adolescent learners, n = 23) was empirically investigated. The study design embodied three data collection phases: (1) a pretest measuring self-rated motivation, learning strategies, and social ability; (2) log file data analysis showing actual use of the system features; and (3) a posttest in a form of an email survey. For both groups, the results showed that the level of motivation has a positive effect on activity in the system and the final grade. The learners, who reported to have good time-management strategies, were the most active users of the system. The level of social ability predicted both the number of consecutive comments in the documents and the threads in document-related newsgroup discussions. Log file data analysis showed that user activity in the system was positively related to the final grade in both samples. Results of the posttest showed that all the respondents agreed when asked: (1) if the system brought added value to the learning process; (2) if the use of the system changed their studying habits favourably; and (3) if they would like to use the system in other courses.