Professionals in the environmental domain require cognitive interdisciplinary skills to be able to develop sustainable solutions to environmental problems. We demonstrate that education in environmental systems analysis allows for the development of these skills. We identify three components of cognitive interdisciplinary skills: (1) the ability to understand environmental issues in a holistic way, taking into account the interplay of social and biophysical dynamics; (2) the ability to connect both the analysis of environmental problems and the devising of solutions with relevant disciplinary knowledge and methodologies; and (3) the ability to reflect on the role of scientific research in solving societal problems. Environmental systems analysis provides tools, methods and models to assist in framing complex environmental issues in a holistic way and facilitates the integration of disciplines. Systems analysis also supports reflection by making students aware that a system always represents a simplified model and a particular perspective. Through the analysis of a collection of BSc students' ‘reflection papers’ we identify two major challenges in teaching these cognitive skills: (1) to train students to not just follow a systematic approach but acquire a systemic view; and (2) to train students to be reflexive about systems analysis and the role of science. We recommend that training in cognitive skills starts early in a study program.