During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and similar to 40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N(2)production by denitrification and anammox were likely linked to sinking organic matter fluxes andin situprimary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N2O and N-2 production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed similar to 10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N(2)production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.