The possible occurrence of reducing microsites in synthetic soil aggregates and their influences on the distribution of selenium species with redox‐dependent mobilities was tested using the synchrotron X‐ray fluorescence microprobe (SXRFM). Synthetic, effectively two‐dimensional soil aggregates of diameters ranging from 10 to 30 mm were constructed, with and without inclusion of sections ofScirpus robustusandS. californicusroot sections. Each aggregate was uniformly wetted with a saline solution containing 240 g m‐3Se [98% as Se(VI), and 2% as Se(IV)]. Gasphase porosities varied between individual aggregates from 0.00 to 0.40 and were maintained relatively constant during the incubation period of up to 17 days. Exchanges of soil gases with atmospheric air occurred only along the periphery of the aggregates. Scanning of the aggregates using SXRFM demonstrated that Se was essentially homogeneously distributed in soils withoutScirpusroot sections, suggesting that Se remained primarily as the soluble Se(VI) species. The SXRFM results revealed large accumulations oftotalSe in regions surrounding embedded sections ofScirpusroots. As much as 20‐fold local enrichment with respect to total Se was measured in water‐saturated soils within 1 to 4 mm of decomposing roots. These observations provide support for a model of localized reducing zones in which Se(VI) is reduced to less mobile Se(IV) and to insoluble Se(0), resulting in local accumulation of total Se. The measured Se accumulation in one microsite compared reasonably well with a simple transient Se(VI) diffustion model. It is postulated that such mechanisms may account for similar heterogeneities observable in some Se‐contaminated soils at Kesterson Reservoir. Such heterogeneities in concentrations of Se and other constituents within individual soil aggregates have important implications with respect to reactivity and need to be included in any detailed mechanistic modeling of chemical cycling within soils. This work also provides an example of the substantial capabilities of SXRFM in studies of soils.