Natural arsenic contamination of groundwater is a severe public health crisis affecting nearly 60 million people in South Asia and Southeast Asia alone. Contamination is spatially heterogeneous and results from the coupled microbial decomposition of organic matter and reductive dissolution of arsenic-bearing iron minerals. Here we demonstrate that elevated arsenic concentrations arise in regions of recent organic matter deposition and thus are controlled by fluvial geomorphic processes. Arsenic contamination is best expressed within recent geomorphic features such as docked islands, scroll bars, and avulsions. Within these features, the deposition of rapidly buried reactive organic matter facilitates microbial iron reduction and arsenic release. Ultimately, the organic matter supply is exhausted and the conditions necessary for soluble arsenic to persist diminish.