Our results show that students rarely employ scientific principles successfully when reasoning about the carbon cycle. When asked to explain familiar processes such as plant and animal growth, animal movement, or flames burning, we found that students frequently refer to the needs and “natural tendencies” of organisms or objects rather than principles of conservation of energy and mass. Accurate accounts of processes at both molecular and global scales are difficult for students with such a conception. For example, a pervasive refrain in student responses links plants and animals in a mutually fulfilling “carbon-oxygen” cycle in which animals breathe in oxygen and breathe out carbon dioxide while plants do the reverse. Our evidence shows that this conception can cause students to confuse the dangers of rising atmospheric carbon dioxide with running out of global oxygen. We are also exploring the importance of quantitative and graphical reasoning skills and students’ capacities for applying scientific reasoning in their personal investigations and decisions as citizens confronting the issue of human impacts on carbon and climate. Insights from our research will be used to inform innovative teaching strategies essential for improving environmental literacy in an era of climate change.