Given the role of Se as both an environmental contaminant and a micronutrient, the microbial reduction and subsequent sequestration of bioavailable Se in soils are of great ecological interest. Primary particles in surface soils are typically bound into loosely packed, microporous aggregates, which may be critical spatial units in determining the fate of Se in soils. Surrounded by macropores where preferential flow rapidly advects dissolved compounds, soil aggregates are domains of slow diffusive transport where spatial variations in chemical concentrations and biogeochemical reactions can prevail. We conducted a series of controlled flow-through experiments utilizing three-dimensional, artificial soil aggregates (2.5-cm i.d.) surrounded by a macropore. Aggregates were composed of either quartz sand or ferrihydrite-coated sand inoculated with one of two Se-reducing bacteria (Thauera selenatis or Enterobacter cloacae SLD1a-1). Selenite export rates varied between 0.02 ± 0.01 and 3.4 ± 0.2 nmol h−1 g−1 as a function of aeration condition and input solution composition (higher SeO42− or C-source concentrations led to higher SeO32− export). Oxic input conditions significantly decreased Se reduction; however, the detection of SeO32− in effluent samples indicates the occurrence of anoxic microzones within aggregates. Furthermore, we found that solid-phase concentrations of reduced Se increased toward the core of aggregates and are estimated to at least double within the first millimeter into the aggregate under all conditions investigated. This indicates that concentrations of reduced Se may generally be expected to increase with distance from the advection boundary (macropore) inside aggregates, which would imply that soils with larger aggregates retain more Se.