The deep waters of the East African Rift Lake Kivu contain large amounts of dissolved carbon dioxide and methane. The release of a fraction of these gases, which could be triggered by a magma eruption within the lake, would have catastrophic consequences for the two million people living on its shore. Up to now the safety assessment of the lake was based on the assumption that the gas concentrations in the deep waters are in a steady state with a residence time of 400 years. Turbulent transport was regarded as the main pathway of vertical exchange. Recent measurements and the analysis of the vertical transport processes in the lake radically change this evaluation. The vertical turbulent exchange is negligible, as documented by a spectacular set of several hundred double-diffusive layers. Gases are mainly transported out of the deep zones by a slow upwelling with a residence time of 800–1000 years. Our results indicate that the methane production within the sediment has recently increased, leading to a gas accumulation in the deep waters and consequently decreasing the heat input needed to trigger a devastating gas release. With the estimated current CH₄ production, the gas concentrations could approach saturation within this century.