<p>Aquifer sediments, which are formed under varying depositional conditions, exhibit significant heterogeneity in their sedimentary architecture, causing variability in their hydraulic and biogeochemical properties. The spatial arrangement of these properties controls the net turnover of biogeochemically reactive and environmentally relevant solutes in floodplains. However, the interlinkage between reactive and hydraulic properties is still enigmatic. This study proposes using sedimentary facies analyses to reconstruct the paleoenvironmental conditions that control the abundance and spatial distribution of aquifer materials, their potential as electron donors and their hydraulic conductivity. The approach was applied to a Holocene aquifer in the Ammer floodplain in southwestern Germany, which mainly consists of organic-rich tufa successions with varying total organic carbon (TOC) content, peat lenses, as well as of gravel and clay layers. The spatial extent of sedimentary features and baseline reactive properties (TOC and hydraulic conductivity) was constrained by combining sedimentological observations and bulk geochemical analyses. Unlike most biogeochemical and hydrogeological studies, bioindicators were included to define the paleoenvironmental conditions and related properties of 11 distinct sedimentary facies types. Based on the insights gained from the paleoenvironmental reconstruction, a facies-based virtual aquifer resembling the sedimentological characteristics of the Ammer floodplain was generated and used to perform 3D flow and transport simulations, using groundwater exposure to TOC as a proxy for reactivity. The study demonstrates that the spatial arrangement of facies, along with their combined biogeochemical and hydraulic properties determines which range of nitrate breakthrough times is to be expected, highlighting the importance of sedimentological insights for groundwater quality projections.</p>