The chemical speciation of arsenic in sediments and porewaters of aquifers is the critical factor that determines whether dissolved arsenic accumulates to potentially toxic levels. Sequestration of arsenic in solid phases, which may occur by adsorption or precipitation processes, controls dissolved concentrations. We present synchrotron x-ray absorption spectra of arsenic in shallow aquifer sediments that indicate the local structure of realgar (AsS) as the primary arsenic-bearing phase in sulfate-reducing conditions at concentrations of 1-3 mmol(.)kg(-1), which has not previously been verified in sediments at low temperature. Spectroscopic evidence shows that arsenic does not substitute for iron or sulfur in iron sulfide minerals at the molecular scale. A general geochemical model derived from our field and spectroscopic observations show that the ratio of reactive iron to sulfur in the system controls the distribution of solid phases capable of removing arsenic from solution when conditions change from oxidized to reduced, the rate of which is influenced by microbial processes. Because of the difference in solubility of iron versus arsenic sulfides, precipitation of iron sulfide may remove sulfide from solution but not arsenic if precipitation rates are fast. The lack of incorporation of arsenic into iron sulfides may result in the accumulation of dissolved As(III) if adsorption is weak or inhibited. Aquifers particularly at risk for such geochemical conditions are those in which oxidized and reduced waters mix, and where the amount of sulfate available for microbial reduction is limited.