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Amazonian populations are increasingly exposed to climatic shocks, yet knowledge of related health impacts is limited. Understanding how health risks are coproduced by local climatic variability, place and social inequities is vital for improving decision-making, particularly in decentralized contexts. We assess the impacts of rainfall variability and multiscale vulnerabilities on birth weight, which has lifelong health consequences. We focus on highly river-dependent areas in Amazonia, using urban and rural birth registrations during 2006–2017. We find a strong but spatially differentiated relationship between local rainfall and subsequent river-level anomalies. Using Bayesian models, we disentangle the impacts of rainfall shocks of different magnitudes, municipal characteristics, social inequities and seasonality. Prenatal exposure to extremely intense rainfall is associated with preterm birth, restricted intra-uterine …