This prospective, longitudinal cohort study examined the effects of flood-related stress in pregnancy on the trajectory of children's motor development; and the moderating effects of gestational timing of the flood or sex of the child. Women who were pregnant during a severe flood reported on their objective flood-related experiences, emotional reactions, and cognitive appraisal of the disaster. At 2-, 6-, 16-months, 2½- and 4-years postpartum, mothers’ assessed their children's fine and gross motor development using the Ages and Stages-3 Questionnaire. High objective flood-exposure, or a negative appraisal, especially in later pregnancy, predicted poorer gross motor skills which rapidly improved across early childhood. Children's fine motor skill was influenced by the sex of the child with improvements in girls’ fine motor skills over time, but not boys’. This demonstrates that stress in pregnancy has enduring influences on gross, but not fine, motor skills. Results are discussed in relation to fetal programming and stress appraisal theory.