Double-diffusive staircases with a total of 230–350 mixed layers and sharp interfaces were observed in nine microstructure temperature profiles measured during February 2004 in Lake Kivu. The presence of these staircases at depths > 120 m indicates that diapycnal turbulent mixing is weak and vertical diffusive transport is dominated by double diffusion. Contrary to previously investigated natural or laboratory double-diffusive systems, the dissolved gases CO2 and CH4 contribute significantly to the density stratification, thereby influencing the formation and the structure of the staircases. The density ratio (i.e., the ratio of the stabilizing effect of dissolved substances to the destabilizing effect of temperature) ranges between 2.0 and 4.5 in large sections of the deep waters, implying a high susceptibility to the formation of staircases. The mixed layers (average thickness 0.48 m) are shown to be in a state of active convection. The average thickness of the interfaces (0.18 m) is surprisingly constant and independent of the large-scale stratification. The vertical heat fluxes correlate well with the temperature steps across the interfaces. Lake Kivu receives inflows from subaquatic springs at several depths that maintain the large-scale structure of the density stratification and disturb the staircases. In comparison to earlier observations from 1972, the double-diffusive heat fluxes appear to have been reduced, leading to a heat accumulation in the deep waters. Conversely, the strengthening of the main chemocline indicates an increased discharge of the subaquatic springs that could be responsible for recent changes in the nutrient cycling and methane production in the lake.