Research shows that prenatal maternal stress (PNMS) negatively affects a range of infant outcomes; yet no single study has explored the effects of stress in pregnancy from a natural disaster on multiple aspects of infant neurodevelopment. This study examined the effects of flood‐related stress in pregnancy on 6‐month‐olds' neurodevelopment and examined the moderating effects of timing of the stressor in gestation and infant sex on these outcomes. Women exposed to the 2011 Queensland (Australia) floods in pregnancy completed surveys on their flood‐related objective and subjective experiences at recruitment and reported on their infants' neurodevelopment on the problem solving, communication, and personal–social scales of the Ages and Stages‐III at 6 months postpartum (N = 115). Interaction results showed that subjective flood stress in pregnancy had significantly different effects in boys and girls, and that at high levels of stress girls had significantly lower problem solving scores than boys. Timing of the flood later in pregnancy predicted lower personal–social scores in the sample, and there was a trend (p < .10) for greater objective flood exposure to predict lower scores. PNMS had no effect on infants' communication skills. In conclusion, differential aspects of maternal flood‐related stress in pregnancy influenced aspects of 6‐month‐olds' neurodevelopment.