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Recent science education reforms, as described in the Framework for K-12 Science Education (NRC, 2012), call for three-dimensional learning that engages students in scientific practices and the use of scientific lenses to learn science content. However, relatively little research at any grade level has focused on how students develop this kind of three-dimensional knowledge that includes crosscutting concepts. This paper aims to contribute to a growing knowledge base that describes how to engage students in three-dimensional learning by exploring to what extent elementary students represent the crosscutting concept systems and system models when engaged in the practice developing and using models as part of an NGSS-aligned curriculum unit. This paper answers the questions: How do students represent elements of crosscutting concepts in conceptual models of water systems? How do students’ representations of crosscutting concepts change related to different task-based scaffolds? To analyze students’ models, we developed and applied a descriptive coding scheme to describe how the students illustrated the flow of water. The results show important differences in how students represented system elements across models. Findings provide insight for the kinds of support that students might need in order to move towards the development of three-dimensional understandings of science content.