Exposure to environmental sources and altered physiological processes of manganese uptake during pregnancy and its possible effect on prenatal and postnatal development are of concern. This study investigates manganese blood levels at the time of delivery across four cohorts of pregnant women residing in coastal communities of South Africa and examines birth outcomes and environmental factors that could influence manganese levels in the study population. The geometric mean (GM) manganese blood levels (MnB) for all women at delivery was 15.2 µg/L. Collectively, rural women reported higher MnB concentrations (GM, 16.1 µg/L) than urban women (GM, 13.5 µg/L, p<0.001). Of the 302 cord blood samples drawn from the study participants (rural women only), GM MnB levels reported for three rural sites were 25.8 µg/L (Rural 1), 33.4 µg/L (Rural 2) and 43.0 µg/L (Rural 3) and were twice as high as their respective maternal levels. However, no significant correlations were found between maternal and cord MnB levels across the 3 study areas. Factors associated 2 with elevated maternal MnB levels, after adjusting for gestational age were: women living in a rural area (Rural 2) (p = 0.021); women drinking potable water from an outdoor/communal tap sourced from municipality (p = 0.021); drinking water from river/stream (p = 0.036); younger maternal age (p = 0.026); consuming leafy vegetables once a week (p = 0.034); and elevated maternal blood lead concentrations (PbB) (p = 0.002). The results indicate that a MnB concentration in rural women during pregnancy is higher compared to urban women and increases with manganese intake from food and water.