Classroom discussions have become a centerpiece of reform efforts in science education because talk mediates the joint co-constructing of knowledge in science classrooms. Although decades of research underscore the importance of talk in supporting science learning, the science education community continues to grapple with how to support teachers and students in navigating the uncertainty that is associated with doing knowledge building work. To address these challenges, we must examine not just "what" gets constructed (the scientific ideas), but "how" knowledge is co-constructed by teachers and students (the process of building those ideas) amidst uncertainty. In this study, we propose a conceptual tool for identifying organizational, epistemic, and interpretive metadiscourse markers (MDMs) in science talk. We highlight how teachers and students use these three types of MDMs as they navigate uncertainty while connecting ideas within and across multiple turns of talk, leveraging resources for knowledge building, and making interpretations about one another's ideas. We conclude with a set of suggestions for how researchers and teachers can utilize this framework to attend to the ways that MDMs index the organizational, epistemic, and interpretive dimensions of uncertainty in the knowledge building process.