Acid mine drainage (AMD) discharge has severe, long lasting impacts on water quality and stream ecology in affected watersheds due in part to the dynamic relationship between toxic metals (e.g. Al, Mn, and Cu) and Fe(III) oxy-hydroxides. Localized areas of biogeochemical activity that can mediate mineralogical transformation changes and cause metal release are potentially linked to stream geomorphology. This relationship has not been previously considered with respect to potential longitudinal variation within an impacted stream. The current work aims to determine how Fe(III) (oxy)-hydroxide speciation and distribution, and pore water chemistry in an AMD-impacted streambed, are affected by the presence of two geomorphic structures (a debris dam and step-pool sequence) in an Ohio watershed impacted by historical coal mining. In terms of solid phase mineralogy and geochemistry, in both the tributary and main stem, goethite was the dominant Fe-bearing phase throughout the AMD deposit depth in cores taken upstream of the geomorphic structures, whereas poorly-crystalline phases dominated downstream of the structures, despite the presence of Fe in the reducible fraction. The concentrations and distribution of extractable Al, Mn, and Cu were also different upstream versus downstream of each structure. Pore water Fe and Mn concentrations were higher downstream of the structures than upstream. Strong downward hydraulic gradients were present above the debris dam and in step-pool 1, whereas weaker upward hydraulic gradients were present below the debris dam and in step-pool 2. This work highlights that AMD deposit speciation and distribution, and pore water chemistry, are not spatially uniform within stream reaches, potentially as a result of groundwater-stream exchange-facilitated interactions in the presence of AMD-derived materials.