Iron and sulfur cycling is an important control on contaminant fate and transport. We present the effects of soil structure, specifically the presence of a soil layer, on linked biogeochemical and hydrological processes involving Fe and S cycling in the vadose zone using repacked soil columns. Synthetic rainwater was applied to a homogenized medium-grained sand column, a homogenized organic-rich loam column, and a sand-over-loam layered column. Water samples were voltammetrically analyzed for total sulfide, Fe2+, and aqueous FeS clusters (FeSaq) using a mercury drop electrode. Aqueous FeS clusters were observed in the loam and layered columns, with the greatest concentrations of FeSaq occurring at the sand–loam interface in the layered column. Redox potential (Eh) measurements showed rapid cycling of redox conditions at the interface (hours to days) suggesting that FeSaq formation was favored under conditions of disequilibrium. However, the relative stability and aqueous nature of FeSaq allowed for it to be transported, which has broader implications for chemical fate and transport in the vadose zone. The co-occurrence of FeSaq with iron-rich soil aggregates near the sand-loam interface in the layered column suggest that FeSaq may act as a precursor to the formation of aggregates that, in our column, subsequently caused an order of magnitude decrease in hydraulic conductivity. These findings suggest that FeSaq should be considered when predicting the transport of contaminants, particularly metals that may associate with FeSaq, in systems with prominent iron and sulfur cycling.