Most environmental issues involve near-surface earth systems that often exhibit complex spatial characteristics and dynamics. Conceptual understanding of complex earth systems influences the development of effective policy and management strategies. Students, like all people, organize knowledge and reason about environmental issues through manipulation of mental models. A mental model is a relatively enduring and accessible, but limited, cognitive representation of an external natural phenomenon. The nature of near-surface earth systems may present major cognitive difficulties to students in their development of authentic, accurate mental models of earth systems. These cognitive difficulties include conceptualization of natural earth environments as systems, understanding the complex characteristics of these systems, and the application of conceptual models of complex earth systems to support environmental problem solving. This paper reviews the nature of near-surface earth systems that exhibit complex behavior and the cognitive and epistemological issues that students may experience in understanding these systems. Finally, I suggest that the same learning issues that students face in the classroom also are encountered by experts, policy managers, and stakeholders while they develop solutions to environmental problems. Therefore, educational research of student learning in earth science may not only support the development of improved pedagogical practices and learning environments, but this research may also support improved environmental decision making.