Arsenic contamination in groundwater from crystalline basement rocks in West Africa has only been documented in isolated areas and presents a serious health threat in a region already facing multiple challenges related to water quality and scarcity. We present a comprehensive dataset of arsenic concentrations from drinking water wells in rural Burkina Faso (n = 1498), of which 14.6% are above 10 μg/L. Included in this dataset are 269 new samples from regions where no published water quality data existed. We used multivariate logistic regression with arsenic measurements as calibration data and maps of geology and mineral deposits as independent predictor variables to create arsenic prediction models at concentration thresholds of 5, 10 and 50 μg/L. These hazard maps delineate areas vulnerable to groundwater arsenic contamination in Burkina Faso. Bedrock composed of schists and volcanic rocks of the Birimian formation, potentially harbouring arsenic-containing sulphide minerals, has the highest probability of yielding groundwater arsenic concentrations > 10 μg/L. Combined with population density estimates, the arsenic prediction models indicate that ~ 560,000 people are potentially exposed to arsenic-contaminated groundwater in Burkina Faso. The same arsenic-bearing geological formations that are positive predictors for elevated arsenic concentrations in Burkina Faso also exist in neighbouring countries such as Mali, Ghana and Ivory Coast. This study's results are thus of transboundary relevance and can act as a trigger for targeted water quality surveys and mitigation efforts.