Managed wetlands such as rice paddies, in particular, represent a promising distributed carbon sink that may help to offset presently increasing levels of atmospheric carbon dioxide. Wetlands are characterized by high primary productivity which, when coupled with seasonally-variable water saturation, can lead to disparate carbon pathways leading to CO2 or CH4 flux to the atmosphere and organic and inorganic carbon sequestration. These divergent outcomes are primarily controlled by water saturation, a parameter manipulated in agriculturally managed wetlands such as rice paddies. Under conditions of limited oxygen delivery to soils, iron commonly serves as a dominant contributor to microbial respiration. Ensuring that iron(III) serves as the dominant sink for electron flow from organic carbon ensures a slow rate of metabolism and minimal methane or nitrous oxide emission, both potent greenhouse gases. Here we illustrate through iron amendments and controlled periods of flooding that carbon storage can be increased within soils. We used both litter decomposition and measurement of gas emissions from soils with varying hydrologic cycles and iron oxide treatments to demonstrate means to link carbon oxidation with iron reduction, thereby increasing carbon storage in soils while continuing to minimize undesirable gas emission under water saturated soil conditions conducive to rice production.