Background In June 2013, the city of Calgary, Alberta and surrounding areas sustained significant flooding which resulted in large scale evacuations and closure of businesses and schools. Floods can increase stress which may negatively impact perinatal outcomes and mental health, but previous research is inconsistent. The objectives of this study are to examine the impact of the flood on pregnancy health, birth outcomes and postpartum mental health. Methods Linked administrative data from the province of Alberta were used. Outcomes included preterm birth, small for gestational age, a new diagnoses of preeclampsia or gestational hypertension, and a diagnosis of, or drug prescription for, depression or anxiety. Data were analyzed using a quasi-experimental difference in difference design, comparing flooded and non-flooded areas and in affected and unaffected time periods. Multivariable log binomial regression models were used to estimate risk ratios, adjusted for maternal age. Marginal probabilities for the difference in difference term were used to show the potential effect of the flood. Results Participants included 18,266 nulliparous women for the pregnancy outcomes, and 26,956 women with infants for the mental health analysis. There were no effects for preterm birth (DID 0.00, CI: -0.02, 0.02), small for gestational age (DID 0.00, CI: -0.02, 0.02), or new cases of preeclampsia (DID 0.00, CI: -0.01, 0.01). There was a small increase in new cases of gestational hypertension (DID 0.02, CI: 0.01, 0.03) in flood affected areas. There were no differences in postpartum anxiety or depression prescriptions or diagnoses. Conclusion The Calgary 2013 flood was associated with a minor increase in gestational hypertension and not other health outcomes. Universal prenatal care and magnitude of the disaster may have minimized impacts of the flood on pregnant women.