Objectives Flooding is the most frequent extreme‐weather disaster and disproportionately burdens marginalized populations. This article examines how food and water insecurity, blood pressure (BP), nutritional status, and diarrheal and respiratory illnesses changed during the 2 months following a historic flood in lowland Bolivia. Methods Drawing on longitudinal data from Tsimane' forager‐horticulturalist (n = 118 household heads; n = 129 children) directly after a historic 2014 flood and ~2 months later, we use fixed effects linear regression and random effects logistic regression models to test changes in the markers of well‐being and health over the recovery process. Results Results demonstrated that water insecurity scores decreased significantly 2 month's postflood, while food insecurity scores remained high. Adults' systolic and diastolic BP significantly declined 2 months after the flood's conclusion. Adults experienced losses in measures of adiposity (BMI, sum of four skinfolds, waist circumference). Children gained weight and BMI‐for‐age Z‐scores indicating buffering of children by adults from food stress that mainly occurred in the community closer to the main market town with greater access to food aid. Odds of diarrhea showed a nonsignificant decline, while cough increased significantly for both children and adults 2 months postflood. Conclusions Water insecurity and BP improved during the recovery process, while high levels of food insecurity persisted, and nutritional stress and respiratory illness worsened. Not all indicators of well‐being and health recover at the same rate after historic flooding events. Planning for multiphase recovery is critical to improve health of marginalized populations after flooding.