Rapid exchange of stream water and groundwater in streambeds creates hotspots of biogeochemical cycling of redox-sensitive solutes. Although stream–groundwater interaction can be increased through stream restoration, there are few detailed studies of the increased heterogeneity of water and solute fluxes through the streambed and associated patterns of biogeochemical processes around stream restoration structures. In this study, we examined the seasonal patterns of water and solute fluxes through the streambed around a stream restoration structure to relate patterns of water flux through the streambed to morphology of the channel and biogeochemical processes occurring in the bed. We characterized different biogeochemical zones in the streambed using principal component analysis (PCA) and examined the change in spatial patterns of these zones during different seasons. The PCA results show that two principal components summarized 83% of the variance in the original data set. Streambed pore water was characterized as oxic (indicating production of nitrate), anoxic (indicating sulfate, iron and manganese reduction), or stream-like (indicating there was minimal change in the stream water chemistry in the bed). Regardless of season of the year, anoxic zones were predominantly located upstream of the structure, in a low-velocity pool, and oxic zones were predominantly located downstream of the structure, in a turbulent riffle. We expect structures that span the full channel, are impermeable, and permanent, such as those installed in natural channel design restoration will similarly impact biogeochemical processing in the streambed. The installation of these types of restoration structures may be a way to increase the degree of biogeochemical cycling in stream ecosystems.