Selenium poisoning is a significant health problem in parts of Punjab, India, which is an area of intense agricultural productivity. To determine the complex soil dynamics that control distribution of Se in this area, we measured concentrations and δ(82/76)Se of bulk Se and individual Se pools in four soil profiles. This was compared against δ(82/76)Se of crops and groundwater used for irrigation. The isotopic composition of bulk Se and component Se pools reveal spatial heterogeneity. The bulk δ(82/76)Se show progressively lower values with increasing soil depth indicating the preferential migration of isotopically lighter Se downward through the soil profile. The δ(82/76)Se of water-soluble Se is isotopically heavier than δ(82/76)Se of adsorbed Se, suggesting Se isotope fractionation by reduction prior to scavenging by reactive minerals in the soil. The organically bound Se is isotopically lighter than water-soluble Se and correlates with the C/N ratio at different soil depths. Thus, Se immobilization by redox cycling controls the biogeochemical Se cycle in the soil. Se isotope ratios help to trace biochemical processes of Se in agricultural seleniferous soils and provide an important assessment for better soil management mitigating Se concentrations of ecotoxicological levels.