Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. In Svalbard fjords, we hypothesize that microbes catalyze intense iron and sulfur cycling in low organic matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. Here, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above 12 cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa, and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low organic matter availability. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.