Batch-type leaching experiments were performed on polluted soil contaminated by pyrite cinders to evaluate the effect of indigenous bacteria on arsenic mobilization. The bacteria, under submerged conditions using citrate as the carbon source, enhanced the solubilization of arsenic, iron and manganese. At the same time, 85 mg kg(-1) of copper were abiotically released. Iron reduction significantly (p < 0.05) enhanced the release of arsenic. During 7 days of incubation at high redox potential, the arsenite content increased suggesting aerobic arsenic-resistant bacteria bearing arsC genes as key players for arsenate reduction. Arsenate became prevalent in consequence of arsenic liberation from iron oxides and the lowering of redox potential, driven by citrate, inhibited the growth and activity of arsenate-resistant bacteria. Populations of Bacillus, Pseudomonas, and Geobacter were stimulated by the addition of citrate as evidenced by denaturing gradient gel electrophoresis analysis of 16S rRNA genes. Putative ars genes were retrieved in isolates of Bacillus and Pseudomonas. These isolates were able to reduce 2 mmol l(-1) of arsenate in liquid cultures. These results confirm that microorganisms play an important role in As cycling in soils and highlight the complex role of citrate on biotic and abiotic transformations of inorganic contaminants. The environmental dispersion of arsenic can be retarded by resorption or coprecipitation processes occurring during flooding. Nevertheless, periodic flooding can be a crucial factor for the groundwater quality and the soil-water-plant systems.