In many freshwater ecosystems, the contents of NO3- and SO4(2-) have increased, whereas O2 has been depleted due to the increased acid and nutrient loads. These changes may affect carbon turnover and the dynamics of the major greenhouse gases CO2, CH4, and N2O. We studied the effects of O2, NO3-, and SO4(2-) availability on carbon mineralization, and fluxes of CO2, CH4, and N2O in the sediments of hyper-eutrophic Lake Kevätön, Finland. Undisturbed sediment cores from the deep (9 m) and shallow (4 m) profundal were incubated in a laboratory microcosm with oxic and anoxic water flows with NO3- or SO4(2-) concentrations of 0, 30, 100, 300, and 2000 microM. The carbon mineralization rate (i.e., the sum of released CO2-C and CH4-C) was not affected by the oxidants. However, the oxidants did change the pathways of carbon degradation and the release of CH4. All of the oxidants depressed CH4 fluxes in the shallow profundal sediments, which had low organic matter content. In the deep profundal sediments rich in organic matter, the CH4 release was reduced by O2 but was not affected by SO4(2-) (the effect of NO3- was not studied). There was an increase in N2O release as the overlying water NO3- concentration increased. Anoxia and highly elevated NO3- concentrations, associated with eutrophication, increased drastically the global warming potential (GWP) of the sedimentary gases in contrast to the SO4(2-) load, which had only minor effects on the GWP.