Many pedagogical innovations aim to integrate engineering design and science learning. However, students frequently show little attempt or have difficulties in connecting their design projects with the underlying science. Drawing upon the Cultural-Historical Activity Theory, we argue that the design tools available in a learning environment implicitly shape knowledge development as they mediate students' design actions. To explore the roles of tools in design-science integrated learning environments, this study investigated how secondary students' tool-mediated design actions were linked with their science learning in a tool-rich design environment with minimal explicit guidance. Eighty-three ninth-grade students completed an energy-efficient home design challenge in a simulated environment for engineering design supported by rich design tools. Results showed that students substantially improved their knowledge as a result of designing with the tools. Further, their learning gains were positively associated with three types of design actions--representation, analysis, and reflection--measured by the cumulative counts of relevant computer logs. In addition, these design actions were linked with learning gains in ways that were consistent with their theoretical impacts on knowledge development. These findings suggest that, instead of being passive components in a learning environment, tools considerably shape design processes, and learning paths. As such, tools offer possibilities to help bridge the design-science gap.