High levels of selenium (Se) were detected in the shallow groundwaters in the rural Carpineni region of Moldova. Selenium concentrations in groundwater exceed the maximum allowable limit by 1.5–24 times (range: 15.0–240.0 μg/L). To identify the source of Se in the groundwater, we analyzed the Se content of groundwater, soils, aquifer strata, and stream sediments. Samples were taken from a variety of locations, each of different land use including both rural agricultural regions and urban areas. Neogene middle Sarmatian clays in the Carpineni region contain both elemental and residual Se. Groundwaters in Carpineni are in intimate contact with these easily weathered units, and weathering of aquifer strata leads to increased Se in rural Moldovan groundwaters. Concentrations of soluble Se are low in soils from Carpineni, and Se remobilization in these soils caused by infiltration is a negligible source of Se in the groundwater. Anthropogenic Se sources also occur in rural Moldova and may contribute to Se in groundwater. Sediments from ponds holding waters used to cool the Cuciurgan Power Station, a former coal-burning plant, contained high Se concentrations. Seepage from these ponds, as well as from similar ponds in Carpineni, may occur, although the contribution to the Se budget of the groundwaters may be minor. In the urban regions of Chisinau City, higher soil concentrations of soluble and ligand-exchangeable Se and the low Se concentrations in the Quaternary loess aquifer strata suggest that the Se in groundwaters in Chisinau are derived from anthropogenic sources, including coal burning and domestic waste discharge with Se mobilized from soils during rain events.