The deep-water of the East African Lake Kivu contains large amounts of dissolved methane (~60 km3 STP) and carbon dioxide (~300 km3 STP). To utilize the methane as an energy resource valued at many billion dollars and to reduce the risk of an uncontrolled gas eruption, the governments of the Democratic Republic of the Congo and Rwanda have decided to begin extracting the methane. The Government of Rwanda has issued first concessions for pilot plants to start extraction in the fall 2008. There are two major risks involved with extracting methane from Lake Kivu: (i) disrupting the lake stratification, which could increase the probability of a gas eruption, and (ii) enhancing the transport of nutrients from the deep-water to the surface water, which could negatively affect the lake ecosystem. These two risks should be kept in mind while trying to (iii) minimize the methane loss and maximize the extraction of the naturally produced methane in the lake. In this study, a one-dimensional model was developed and applied to predict the stratification, in addition to the gas and nutrient concentration profiles, for a 100 year period of various methane extraction Scenarios in Lake Kivu. The goal of the modelling is to find an optimal strategy that acceptably fulfils all three concerns (safety, lake ecology and socioeconomic benefit). The resulting simulations let us conclude that (a) the deep-water MUST NOT be diluted with surface water to adjust its density before reinjection into the lake, and that (b) the degassed deep-water can not be reinjected above 200 m depth, where this would lead to both strongly increased nutrient fluxes into the surface layer and unacceptable algae growth. Despite these two restrictions it is possible to harvest ~90% of the maximal possible methane without risking a gas eruption and without sacrificing the ecological integrity of the lake. The key findings are listed in the executive summary.