Background: Design and science inquiry are intertwined during engineering practice. In this study, we examined the relationship between design behaviors and scientific explanations. Data on student design processes were collected as students engaged in a project on designing energy-efficient buildings on a blank square city block surrounded by existing buildings using a computer-aided design program, Energy3D, with built-in solar energy simulation capabilities. We used criterion sampling to select two highly reflective students among 63 high school students. Results: The main data sources were design replays (automatic playback of student design sequences within the CAD software) and electronic notes taken by the students. We identified evidence of informed design such as problem framing, idea fluency, and balancing benefits and trade-offs. Opportunities for meaningful science learning through engineering design occurred when students attempted to balance design benefits and trade-offs. Conclusions: The results suggest that design projects used in classrooms should emphasize trade-off analysis and include time and resources for supporting trade-off decisions through experimentation and reflection. Future research should explore ways to visualize patterns of design behavior based on large samples of students.