The accumulation of nutrients (eutrophication) in water bodies generally produces increased concentrations of organic matter that eventually are deposited in sediment, and partially mineralized, generating greenhouse carbon gases (GHCG). The application of eutrophication control methods includes the application of phosphate adsorbing materials such as Phoslock (PHOS), and hypolimnetic oxygenation systems (HOS). We evaluated the generation of GHCG in sediment subject to these eutrophication control methods. Combined water and sediment samples from the Valle de Bravo reservoir in Mexico, were incubated in reactors, where the following eutrophication control methods were applied: HOS, PHOS, HOS + PHOS, and compared to a reactor without treatment (CONTROL). Redox potential (Eh), pH, redox-sensitive ions, and GHCG emissions were monitored, observing the following rates: CONTROL (15.6 mmol m−2 d−1) > HOS (12.8) > HOS + PHOS (11.0) > PHOS (9.7 mmol m−2 d−1), with the CONTROL rate within values determined from published sediment core data. The GHCG emissions increased with time as Eh decreased, and sulfate reduction increased. Application of eutrophication control methods in the Valle de Bravo reservoir, would most probably result in lower GHCG generation and emission rates. This is due to the repression of sulfate-reduction in water-sediment systems where HOS and PHOS were applied both individually and combined.