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This paper examines how transnational scientific networks linking Brazilian, European, and US institutions during the Cold War reshaped knowledge about the structure and functioning of Amazonian ecosystems. It traces how synergies, power asymmetries, colonial legacies, frictions, and negotiations contributed to conceptualizing the Amazon as a unified system articulated through material and energetic fluxes connecting waters, soils, forests, and atmosphere. We focus on the collaborations between the National Institute for Amazonian Research (INPA) and the Max Planck Institutes of Limnology and Atmospheric Chemistry, as well as with the Center for Nuclear Energy in Agriculture (CENA) at the University of São Paulo. We explore how these networks were instrumental in positioning the Amazon within emerging debates that framed the planet as an interconnected environmental system vulnerable to anthropogenic disturbance. By simultaneously advancing ecological research and critiquing state-led development programs, these collaborations defined the region as a threatened biome whose future carried planetary implications. In doing so, they contributed to the historical making of the Amazon as an Anthropocene hotspot: both a site of intensified environmental disruption under extractive regimes and a privileged arena for rethinking the co-production of scientific knowledge, ecology, climate, and global environmental governance.