Ecosystem metaphors are increasingly used to describe complex business and civil society relationships. This article argues that the rise of ecosystem thinking in public policy and administration represents a new, radically decentred model of policy action. It focuses on ecosystems of data-driven modelling and experts who use government public health data. This study presents a conceptual framework that suggests effective data ecosystems undergo organic adaptation, display institutional leadership, and respond instrumentally to policymakers’ information needs. It examines how Australia’s infectious disease data ecosystem performed before and during the COVID-19 pandemic. In-depth interviews with data experts involved in infectious disease modelling in Australia revealed trade-offs within and between organic, institutional and instrumental dimensions, which COVID-19 exacerbated. The article concludes that data ecosystems represent a hybrid form of policymaking in practice and that tensions must be managed to maximise the contributions of data ecosystems to facilitate evidence-informed decision-making.