Groundwater from the Mississippi River Valley alluvial aquifer (MRVA) is a vital resource for agriculture and drinking-water supplies in the central United States. Water availability can be limited in some areas of the aquifer by high concentrations of trace elements, including manganese and arsenic. Boosted regression trees, a type of ensemble-tree machine-learning method, were used to predict manganese concentration and the probability of arsenic concentration exceeding a 10 µg/L threshold throughout the MRVA. Explanatory variables for the BRT models included attributes associated with well location and construction, surficial variables (such as hydrologic position and recharge), variables extracted from a MODFLOW-2005 groundwater-flow model for the Mississippi embayment, and variables from an airborne electromagnetic survey of the aquifer. This data release provides the R scripts to tune and reproduce the BRT models and final prediction rasters. For a full description of modeling workflow and final model selection see the companion journal article.