A critical agenda for earth and life sciences is to determine how diverse tropical marine ecosystems such as coral reefs will respond to global environmental change. This will require long-term environmental and ecological data that rarely exist for living coral reefs. In contrast, the fossil record provides abundant examples that can be mined to predict future outcomes. The THROUGHFLOW network will train a cohort of eleven ESRs to enable them to reconstruct past environments and patterns of biotic change using up-to-date technologies within a collaborative interdisciplinary framework. The training program will explore the past record of change on coral reefs in SE Asia in response to reorganization of ocean currents during the Cenozoic. This region contains both the Indo-West Pacific Center of Biodiversity (the most diverse shallow marine ecosystems on Earth) and the Indonesian Throughflow (a primary control of global climate). THROUGHFLOW will reconstruct the history of these two features and develop a model for how coral reefs respond to regional environmental change. Practical training will include eleven integrated research projects and a series of joint training activities to facilitate collaboration and provide access to a variety of expertise. THROUGHFLOW will bring important new data to bear on long-standing scientific controversies, and the results will be relevant to a broad audience including industry and policy makers working to predict and plan for the effects of ongoing anthropogenic environmental change. By providing rigorous training in a range of applied techniques in geology and biodiversity, THROUGHFLOW will produce researchers able to pursue successful careers in academia or industry and will enhance the power of the European research community to tackle pressing issues related to the effects of ongoing environmental change on the biosphere.