Lake Kivu in East Africa has gained notoriety for its prodigious amounts of dissolved methane and dangers of limnic eruption. Being meromictic, it is also expected to accumulate heat due to rising regional air temperatures. To investigate the warming trend and distinguish between atmospheric and geothermal heating sources, we compiled historical temperature data, performed measurements with logging instruments, and simulated heat propagation. We also performed isotopic analyses of water from the lake's main basin and isolated Kabuno Bay. The results reveal that the lake surface is warming at the rate of 0.12°C per decade, which matches the warming rates in other East African lakes. Temperatures increase throughout the entire water column. Though warming is strongest near the surface, warming rates in the deep waters cannot be accounted for solely by propagation of atmospheric heat at presently assumed rates of vertical mixing. Unless the transport rates are significantly higher than presently believed, this indicates significant contributions from subterranean heat sources. Temperature time series in the deep monimolimnion suggest evidence of convection. The progressive deepening of the depth of temperature minimum in the water column is expected to accelerate the warming in deeper waters. The warming trend, however, is unlikely to strongly affect the physical stability of the lake, which depends primarily on salinity gradient.