Amazonian populations are increasingly exposed to climatic shocks yet knowledge of related health impacts is limited. Understanding how health risks are co-produced 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 multi-scale vulnerabilities on birth-weight, which has life-long 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 growth and lower mean birth-weight (≤-183g). Adverse birth outcomes also follow non-extreme intense rainfall (40% higher odds of low birth-weight), drier than seasonal averages (-39g mean birth-weight) and conception in the rising-water season (-13g mean birth-weight). Babies experience penalties totalling 646g when born to adolescent, Amerindian, unmarried mothers that received no formal education, antenatal or obstetric healthcare. Rainfall variability confers inter-generational disadvantage, especially for socially-marginalized Amazonians in forgotten places. Structural changes are required to reduce inequities, foster citizen empowerment, and improve the social accountability of public institutions.