The National Science Education Standards have highlighted the importance of active learning and reflection for contemporary scientific methods in K–12 classrooms, including the use of models. Computer modeling and visualization are tools that researchers employ in their scientific inquiry process, and often computer models are used in collaborative projects across disciplines. The goal of this project was to develop and field-test a module that used a computer model to teach marine sciences content in an applied, inquiry-based, and collaborative manner. Students used an estuarine transport model to explore the question of how circulation patterns affect planktonic organisms, demonstrating the interdisciplinary interaction of physics and biology. Our experience suggests that computer models, when used for inquiry, can help foster students' understanding of the nature of science and critical-thinking skills.