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Recent reforms in science education have supported the inclusion of engineering in K- 12 curricula. To this end, many science classrooms have incorporated engineering units that include design tasks. Design is an integral part of engineering and helps students think in creative and interdisciplinary ways. In this study, we examined middle-school students’ naturally occurring design conversations in small design teams and their learning of science as a result of engaging in an engineering and science unit. We found that the proportion of different thought processes used by boys and girls was quite similar. Both girls and boys produced a higher percentage of ideas or thoughts associated with divergent thinking, but a lower proportion in convergent thinking, evaluative thinking, and cognitive memory. In addition, gender composition of design teams influenced thought processes expressed by girls and boys. Interestingly, in mixed teams, both girls and boys expressed less divergent thinking than those in single-sex teams. With regard to science content learning, both girls and boys showed statistically significant learning gains. There were no significant gender differences in the pre- and post-test scores. These results suggest that participating in an engineering design task in small design teams provided students opportunities to engage in productive thinking and enhance their learning of the targeted science concept—ecosystems.