Given the importance of fresh water, we investigated undergraduate students’ understanding of water flow and its consequences. We probed introductory geology students’ pre-instruction knowledge using a classroom management system at two large research-intensive universities. Open-ended clicker questions, where students click directly on diagrams using their smart device (e.g., cell phone, tablet) to respond, probed students’ predictions about: (1) groundwater movement and (2) velocity and erosion in a river channel. Approximately one-third of students correctly identified groundwater flow as having lateral and vertical components; however, the same number of students identified only vertical components to flow despite the diagram depicting enough topographic gradient for lateral flow. For rivers depicted as having a straight channel, students correctly identified zones of high velocity. However, for curved river channels, students incorrectly identified the inside of the bend as the location of greatest erosion and highest velocity. Systematic errors suggest that students have mental models of water flow that are not consistent with fluid dynamics. The use of students’ open-ended clicks to reveal common errors provided an efficient tool to identify conceptual challenges associated with the complex spatial and temporal processes that govern water movement in the Earth system.