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The rise of oxygen in the early Earth atmosphere allowed for a vast expansion of life, including the proliferation of animal life, that could utilize this powerful electron acceptor for new metabolisms. This oxygen requirement has left many organisms vulnerable to oxygen-depleted conditions (i.e., anoxia). These anoxic events in Earth’s aquatic environments allow for free iron (ferruginous) or free sulfide (euxinic) conditions to develop. While much research has been done on the past and present of aquatic anoxia, transiently deoxygenated systems that cycle annually between oxygenated and anoxic states are underexplored. Questions about these cycles of aquatic redox state abound; for example, 1) if benthic sulfur-oxidizing bacteria promote free sulfide at the sediment-water interface in transiently deoxygenated systems 2) if these cycles of anoxia can promote a loss of free iron from the benthic marine environment and 3) if sulfate reducing bacteria are quickly established in lacustrine waters after anoxia develops. The first and second questions will be addressed in this dissertation through a suite of investigations in the transiently deoxygenated Santa Barbara Basin. Porewater geochemistry, sulfate reduction rates, and benthic flux measurements were collected between 2019-2023 under varying oxygen concentrations. We found that sulfur-oxidizing bacterial mats in the basin are associated with high rates of dissimilatory nitrate reduction to ammonium and require an elevation of the sulfate reduction zone to the sediment-water interface in order to proliferate. Mat proliferation also requires an exhaustion of iron oxides in the surface sediment. Mat formation is also associated with extremely high fluxes of iron into the water column. This free iron is potentially lost from the basin through bottom water currents that carry mid-waters upslope during the anoxic events.The third question will be addressed in this dissertation by several geochemical and ex-situ sulfate reduction measurements taken in the Salton Sea between 2020-2023 under a variety of water column redox conditions. We found that sulfate reduction is present in waters that contained oxygen, most likely occurring inside organic particles in the water. We also found that sulfate reduction is quickly established after the onset of anoxia in the lake.