Manganese is a very reactive redox metal, which exhibits a strong annual cycle in Oneida Lake, New York. Different methods were used to measure Mn(II) fluxes from the sediments throughout the year: (1) estimates based on changes in porewater profiles, (2) direct measurements with in situ flux chambers, (3) concentration gradients into the sediment–water interface in laboratory-incubated cores, and (4) changes in hypolimnetic manganese inventories during stratification. In deep basins of the lake, high rates of Mn(IV) reduction, up to 2.1 mmol∙m−2∙d−1, were observed during the summer and early fall, with little reduction taking place during the rest of the year. In the shallow areas of the lake, where ferromanganese nodules and crusts are commonly found, there was little or no reduction throughout the year. The manganese cycle is tightly coupled to the carbon cycle, based on our findings, and has a significant role in the oxidation of organic carbon in the lake, derived from the high photosynthetic production and the bio-mass that collapses and reaches the sediment–water interface. Preliminary experiments with poisoned controls suggest that Mn(IV) reduction is the result of a combination of biological and abiological processes.