Recent education reforms highlight the importance of engineering design as a tool to improve student science learning in this new view of K-12 science education. However, little research has investigated the thought processes students use while engaging in the highly complex activity of design. Therefore, building on theories of productive thinking, we analyzed 6th grade students' design conversations through the following research question: How do 6th grade students employ different modes of thinking when solving a design-based challenge in a science unit? Through a qualitative and descriptive case-study approach using Gallagher and Aschner's (Merrill-Palmer Q Behav Dev 9(3):183-194, 1963) analytical framework for productive thinking, our results indicate students employ a variety of modes of thinking as they engage in design conversations in a science-based design unit. While students planned their initial design, they employed Cognitive Memory, Divergent Thinking, and Evaluative Thinking. This is not surprising since students need to recall scientific facts and hypothesize as they begin to justify their design decisions. As students finalized design decisions and communicated this design to the client, they employed more higher order modes of thinking, since they evaluated and justified their design decisions. These findings provide insights into effective teaching strategies for higher productivity and conceptual performance.