The Sustainable Development Goals (SDGs) aim to elicit global mobilization to implement the 2030 Agenda for Sustainable Development, and are increasingly used in support of Education for Sustainable Development (ESD). Previous studies have highlighted interdependencies between SDGs, with potential interactions between four Sustainability Domains: Economy, Governance, Planet and Society. This study aimed to assess whether people’s perception of the relative importance of the SDGs reflects recognition of the need to prioritize efforts across Domains, or whether this perception is based on different valuations of the Sustainability Domains themselves. We designed an interactive online tool in which participants used the Q-sort technique to rank the SDGs according to their subjective valuation of importance. We analyzed the rankings of 108 participants, all learners at universities in three Small Island States (SIS): Aruba, Suriname and Trinidad and Tobago. Analysis of the correlation structure among participants’ Q-sorts showed that higher perceived importance of the Society- and Economy-related SDGs 2, 3, 4, 8 and 9 traded off with lower perceived importance of the Planet-related SDGs 13, 14 and 15. Furthermore, SDG rankings of learners from Aruba occurred furthest toward the Planet-based part of this trade-off axis. For ESD programs, our method provides a novel tool to identify key interactions between SDGs that may not yet be recognized by program participants. In this way, communicating the need for simultaneous action and policy development across Sustainability Domains could be specifically tailored to the local context. Such connections may increase the effectiveness of ESD in addressing the substantial sustainability challenges facing SIS.