tMany national policy documents underscore the importance of 21st century skills, includ-ing critical thinking. In parallel, recent American frameworks for K-12 science educationcall for the development of critical thinking skills in science, also referred to as scienceinquiry skills/practices. Assessment of these skills is necessary, as indicated in policy doc-uments; however, this has posed a great challenge for assessment researchers. Recently,some science learning environments seek to assess these science skills. These systems logall students’ interactions within the given system, and if fully leveraged, these logs pro-vide rich assessments of inquiry skills. Here, we describe our environment Inq-ITS (inquiryintelligent tutoring system), that uses educational data mining to assess science inquiryskills, as described as 21st century skills. Additionally, here, we describe how we measurestudents’ skills at designing controlled experiments, a lynchpin skill of inquiry, in the con-text of complex systems. In doing so, our work addresses 21st century skill assessment intwo ways, namely of inquiry (designing and conducting experiments), and in the contextof complex systems, a key topic area of 21st century skills. We use educational data miningto develop our assessment of this skill for complex systems.