The origin of dissolved arsenic in the Ganges Delta has puzzled researchers ever since the report of widespread arsenic poisoning two decades ago. Today, microbially mediated oxidation of organic carbon is thought to drive the geochemical transformations that release arsenic from sediments, but the source of the organic carbon that fuels these processes remains controversial. At a typical site in Bangladesh, where groundwater-irrigated rice fields and constructed ponds are the main sources of groundwater recharge, we combine hydrologic and biogeochemical analyses to trace the origin of contaminated groundwater. Incubation experiments indicate that recharge from ponds contains biologically degradable organic carbon, whereas recharge from rice fields contains mainly recalcitrant organic carbon. Chemical and isotopic indicators as well as groundwater simulations suggest that recharge from ponds carries this degradable organic carbon into the shallow aquifer, and that groundwater flow, drawn by irrigation pumping, transports pond water to the depth where dissolved arsenic concentrations are greatest. Results also indicate that arsenic concentrations are low in groundwater originating from rice fields. Furthermore, solute composition in arsenic-contaminated water is consistent with that predicted using geochemical models of pond-water-aquifer-sediment interactions. We therefore suggest that the construction of ponds has influenced aquifer biogeochemistry, and that patterns of arsenic contamination in the shallow aquifer result from variations in the source of water, and the complex three-dimensional patterns of groundwater flow.