We investigated CH4 oxidation in the water column of Lake Kivu, a deep meromictic tropical lake with CH4-rich anoxic deep waters. Depth profiles of dissolved gases (CH4 and N2O) and a diversity of potential electron acceptors for anaerobic CH4 oxidation (NO3 −, SO4 2−, Fe and Mn oxides) were determined during six field campaigns between June 2011 and August 2014. Denitrification measurements based on stable isotope labelling experiments were performed twice. In addition, we quantified aerobic and anaerobic CH4 oxidation, NO3 − and SO4 2− consumption rates, with and without the presence of an inhibitor of SO4 2−-reducing bacteria activity. Aerobic CH4 production was also measured in parallel incubations with the addition of an inhibitor of aerobic CH4 oxidation. The maximum aerobic and anaerobic CH4 oxidation rates were estimated to be 27 ± 2 and 16 ± 8 μmol/L/d, respectively. We observed a difference in the relative importance of aerobic and anaerobic CH4 oxidation during the rainy and the dry season, with a greater role for aerobic oxidation during the dry season. Lower anaerobic CH4 oxidation rates were measured in presence of molybdate in half of the measurements, suggesting the occurrence of linkage between SO4 2− reduction and anaerobic CH4 oxidation. NO3 − consumption and dissolved Mn production rates were never high enough to sustain the measured anaerobic CH4 oxidation, reinforcing the idea of a coupling between SO4 2− reduction and CH4 oxidation in the anoxic waters of Lake Kivu. Finally, significant rates (up to 0.37 μmol/L/d) of pelagic CH4 production were also measured in oxygenated waters.