Selenium (Se) is an essential trace element for animals and displays a narrow range between dietary deficiency and toxicity. The toxicity of Se depends on its bioavailability, which is directly related to its oxidation states, of which four occur in the environment (SeVI, SeIV, Se0 and SeII). Microbial communities drive the cycling of Se between these oxidation states. In order to investigate the effect of microbial activity on Se cycling in the environment, a field site in County Meath, Ireland, was identified with anomalously large concentrations of Se as a result of weathering of black shales within the Lucan formation, leading to cases of Se toxicity in farm animals. Soil cores were extracted from the site for Se speciation and microbial community analysis prior to microcosm experiments to assess Se stability and microbial Se transformations. Selenium was present as a recalcitrant, reduced organic phase that was strongly coordinated with carbon, concordant with suggested hypotheses of Se phyto-concentration within a clay-lined, postglacial marshland. Selenium was not mobilized in microcosm experiments, and supplementation with SeVI resulted in rapid reduction and removal from solution as Se0. Additional electron donors did not affect Se stability or removal from solution, although nitrate did hinder SeVI reduction. Terminal restriction fragment length polymorphism analysis indicated a significant shift in microbial community after amendment with SeVI. This work extends the current knowledge of Se cycling in the environment, and provides information on the bioavailability of Se in the soil, which determines Se content of foodstuffs.