BackgroundGestational diabetes mellitus (GDM) is a major pregnancy complication with detrimental effects for both mothers and their children. Accumulating evidence has suggested a potential role for arsenic (As) exposure in the development of GDM, but current studies have not assessed As exposure from water, urine or toenail samples.MethodsWe investigated the association between As exposure and risk of glucose intolerance and GDM among 1151 women enrolled in the New Hampshire Birth Cohort Study. Arsenic was measured in home well water and via biomarkers (i.e., maternal urine collected ~24–28 weeks gestation and toenail clippings collected 2 weeks postpartum).ResultsA total of 105 (9.1 %) of women were diagnosed with glucose intolerance and 14 (1.2 %) of women were diagnosed with GDM. A total of 10.3 % of women had water As levels above 10 μg/L, with a mean As level of 4.2. Each 5 μg/L increase in As concentration in home well water was associated with a ~10 % increased odds of GDM (OR: 1.1, 95 % CI 1.0, 1.2). A positive and statistically significant association also was observed between toenail As and GDM (OR: 4.5, 95 % CI 1.2, 16.6), but not urinary arsenic (OR: 0.8, 95 % CI 0.3, 2.4). In a stratified analysis, the association between water As and GDM and glucose intolerance was largely limited to obese women (OR: 1.7, 95 % CI 1.0, 2.8).ConclusionsOur findings support the role of As exposure via water from private wells in the incidence of GDM and that this association may be modified by body composition.Electronic supplementary materialThe online version of this article (doi:10.1186/s12940-016-0194-0) contains supplementary material, which is available to authorized users.