Transdisciplinary research is widely being promoted for its potential to effectively address complex issues, such as ecosystem management in a changing climate. Working across disciplines and with broader society can benefit greatly from continuous evaluation to improve transdisciplinary practices. However, methods for such continuous self-reflection are scarce, with little evidence of the application of social science concepts, theory, or methods. This article presents a case study of how researchers from different disciplinary backgrounds have familiarized themselves with the key social science concepts of “structure” and “agency” to reflect on the integrative research efforts of a research center in southwestern Australia. They identified influential “structures” as the geographical separation of the center's research groups, contrasting research cultures, and little previous engagement with the social sciences. Evidence of “agency” comprised various interventions to promote collaboration. Intriguingly, these interventions rendered some challenging paradoxes.