Double diffusion in lakes and oceans can transform vertical gradients into staircases of convectively mixed layers separated by thin stable interfaces. Lake Kivu is an outstanding double-diffusive natural laboratory with > 300 such steps over the permanently stratified deep basin. Here, we use 315 microstructure profiles (225 measured in Rwanda and 90 in the DRC) to shed light on the heat and salt balances of Lake Kivu. Comparing profiles from 2011 and 2015 reveals warming of 8.6 mK yr−1 below 80 m depth and negligible changes in salinity. The double-diffusive layering is coherent over horizontal distances of 20–30 km and remained unchanged between 2011 and 2015, indicating little variability. The mean estimated dissipation within mixed layers is 1.5 × 10−10 W kg−1. If unshaped Batchelor microstructure spectra are interpreted as nonturbulent, the rescaled dissipation of 0.44 × 10−10 W kg−1 corresponds to a vertical heat flux of 0.10 W m−2, which agrees with the molecular heat flux through the adjacent stable interfaces. Using estimates of upwelling, temporal changes of temperature and salt, and vertical double-diffusive fluxes, we established heat and salt balances, which require lateral heat and salt inputs. For salt, lateral input of freshwater at the main gradients balances upwelling. For temperature, however, the divergence of the vertical double-diffusive fluxes can only be balanced by horizontal inputs supplying cool water above and warm water below the main gradients. This suggests that lateral inputs of water at various depths are the main drivers for this unique double-diffusive phenomenon in Lake Kivu.