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The United Nations' Agenda 2030 marks significant progress towards sustainable development by making explicit the intention to integrate previously separate social, economic and environmental agendas. Despite this intention, the Sustainable Development Goals (SDGs) which were adopted to implement the agenda, are fragmented in their formulation and largely sectoral. We contend that while the design of the SDG monitoring is based on a systems approach, it still misses most of the dynamics and complexity relevant to sustainability outcomes. We propose that insights from the study of social-ecological systems offer a more integrated approach to the implementation of Agenda 2030, particularly the monitoring of progress towards sustainable development outcomes. Using five key features highlighted by the study of social-ecological systems (SESs) relevant to sustainable development: (1) social-ecological feedbacks, (2) resilience, (3) heterogeneity, (4) nonlinearity, and (5) cross-scale dynamics. We analyze the current set of SDG indicators based on these features to explore current progress in making them operational. Our analysis finds that 59% of the indicators account for heterogeneity, 33% for cross-scale dynamics, 23% for nonlinearities, and 18% and 17%, respectively, for social-ecological feedbacks and resilience. Our findings suggest limited use of complex SES science in the current design of SDG monitoring, but combining our findings with recent studies of methods to operationalize SES features suggests future directions for sustainable development monitoring for the current as well as post 2030 set of indicators.