Providing model-based accounts (explanations and predictions) of water and substances in water moving through environmental systems is an important practice for environmental science literacy and necessary for citizens confronting global and local water quantity and quality issues. In this article we present a learning progression for water in environmental systems for students in elementary through high school grades. We investigated student accounts of water and substances in water moving through atmospheric, surface, and soil/groundwater systems, including human-engineered components of these systems. Using an iterative process of model design, assessment, and interpretation, we identified four levels of achievement in student reasoning. Levels 1 and 2 force-dynamic accounts explain movement of water as interactions between natural tendencies of water and countervailing powers. Level 3 incomplete school science accounts put events in order and trace water and substance along multiple pathways that include hidden and invisible components. Only Level 4 qualitative model-based accounts include driving forces and constraining factors to explain or predict where water and substances in water move in given situations. The majority of high school students on average provide accounts between levels 2 and 3. We discuss the significance of these results for citizen participation in addressing common water issues. We end with suggestions for how the water learning progression can be used to inform changes to curricula, assessment, and instruction to support students in achieving level 4 performance. (Contains 2 notes, 3 figures and 2 tables.)