Peer collaboration and questioning are two pedagogical methods currently used under the assumption that they facilitate conceptual understanding in science classrooms. However, the literature on peer collaboration reveals many contextual factors that influence the success of peer learning, particularly for ill-structured tasks, and little research has been conducted on whether or how questions help students learn about complex science topics. This study investigated the impact of peer collaboration and reasoning questions on high-school students' (N = 133) conceptual-knowledge learning, through analysis of their regulatory learning processes as they studied the circulatory system using a hypermedia encyclopedia. Outcome variables were a measure of students' conceptual knowledge learning (pretest to posttest) and peers' collaborative discourse, which was collected via audiotape during the learning session. Data analysis consisted of quantitative analyses of variance of students' conceptual knowledge learning in peer and questioning conditions, and qualitative analysis of students' collaborative regulatory discourse. Results revealed variable approaches to collaboration and the task and variable success at conceptual-knowledge learning across pairs. Successful peer learners employed a variety of regulatory behaviors such as taking notes and summarizing to a greater degree than unsuccessful collaborating students, who tended to spend a large proportion of their time off-task. Students who answered an inferential reasoning question spent much of their time looking for a verbatim answer from the environment, often to the detriment of their learning. The results of this study reveal a number of factors that may be related to the success of collaboration and question-answering, including an accurate perception of the task goal; enough relevant prior knowledge about the topic to use a non-linear hypermedia environment effectively; and enough time to collaborate and learn. This study contributes to the literature on collaboration and question-answering by demonstrating the potential pitfalls of these methods and elucidating potential targets for support to bolster the efficacy of these methods.