Water security is strongly associated with important health outcomes and has many socioecological determinants. Several studies have documented the social determinants of water security and impacts of water security on health, independently. Yet few have examined both components in one setting. Using data from Ecuador’s nationally representative health survey (ENSANUT-ECU), we proposed a new methodological framework for assessing water security in the Galápagos and assessed the relationship between socioecological indicators and water security among 2701 individuals in 693 households. We then tested the link between water security and childhood stunting using multilevel mixed effects logistic regressions controlling for household clustering. We found that being higher income in rural settings is significantly protective of water quality (OR 7.35) and increasing household size is associated with reduced water access (OR 0.44). We found no impact of water insecurity on childhood stunting. We observed a marked divergence in water security between islands and discussed potential underlying structural determinants. Understanding the structural predictors of water security and health is a necessary step in improving local health outcomes in the Galápagos. The social and physical factors leading to this water security environment may also be shared by similar locations, broadening the application of these findings.