Iron and manganese transformation reactions greatly impact a variety of environmental and biogeochemical processes in the environment, including the transport and degradation of inorganic and organic contaminants, the cycling of organic carbon, and the transformation a variety of other biogeochemically important chemical species. In addition, as essential nutrient, iron exerts a substantial control on ocean productivity and export of organic matter to the deep ocean. Although the mechanism of dissimilatory metal reduction is still under debate, the cycling of electron shuttling compounds is widely recognized to efficiently transfer electrons to solid terminal electron acceptors. In this dissertation, the ability of thiols to abiotically reduce Fe(III) and Mn(III/IV) oxides was investigated in environmentally relevant conditions, and the role of thiols as electron shuttles was assessed in a variety of freshwater and marine sediments as well as in pure cultures of model Fe(III)- reducing bacteria. Together these studies demonstrated that endogenous or exogenous thiols represent important electron shuttles in microbial metal reduction and that these thiols could be used to identify zones of microbial metal reduction in sediments. Organic complexes of Fe(III), produced either during oxidation of Fe(II) in the presence of dissolved organic ligands or during dissimilatory iron reduction, were pervasive in all sediments investigated. These complexes may diffuse across the sediment-water interface and increase the bioavailability of iron in marine surface waters. Although continental margin sediments have been recognized to represent an important source of iron to the oceans, all studies so far have focused on continental margins with large upwelling or riverine inputs. In this work, the diffusive flux and speciation of iron along a transect across the passive margin of Cape Lookout, NC were assessed to determine the importance of the benthic iron flux in an environment not exposed to significant upwelling or riverine inputs. Results revealed that the main flux of iron to the overlying waters occurs on the continental slope which act as carbon and mineral depocenter. These fluxes extrapolated to the overall ocean indicate that global estimates of iron inputs from continental slope sediments rival those derived from aerosols, rivers, and hydrothermal vents. Overall, this work demonstrated the importance of microbial iron reduction in marine sediments and identified new chemical species that may be used to differentiate microbial from chemical iron reduction in natural sediments.