Unique worldwide, Lake Kivu stores enormous amounts of CH₄ and CO₂. A recent study reported that CH₄ concentrations in the lake have increased by up to 15% in the last 30 years and that accumulation at this rate could lead to catastrophic outgassing by ∼2100. This study investigates the present-day CH₄ formation and oxidation in Lake Kivu. Analyses of ¹⁴C and ¹³C in CH₄ and potential carbon sources revealed that below 260 m, an unusually high ∼65% of the CH₄ originates either from reduction of geogenic CO₂ with mostly geogenic H₂ or from direct inflows of geogenic CH₄. Aerobic CH₄ oxidation, performed by close relatives of type X CH₄-oxidizing bacteria, is the main process preventing CH₄ from escaping to the atmosphere. Anaerobic CH₄ oxidation, carried out by CH₄-oxidizing archaea in the SO₄²⁻-reducing zone, was also detected but is limited by the availability of sulfate. Changes in ¹⁴C_CH₄ and ¹³C_CH₄ since the 1970s suggest that the amount of CH₄ produced from degrading organic material has increased due to higher accumulation of organic matter. This, as well as the sudden onset of carbonates in the 1960s, has previously been explained by three environmental changes: (1) introduction of nonnative fish, (2) amplified subaquatic inflows following hydrological changes, and (3) increased external inputs due to the fast growing population. The resulting enhancement of primary production and organic matter sedimentation likely caused CH₄ to increase. However, given the large proportion of old CH₄ carbon, we cannot exclude an increased inflow of geogenic H₂ or CH₄.