There has been a considerable increase in the pace at which hydrocarbon reserves are being targeted in some of the most remote and pristine areas on our planet, often involving the use of controversial technologies such as hydraulic fracturing or deepwater drilling. Unnoticed by the public, initiatives for oil exploration are advanced in Africas largest freshwater reservoirs, including Lakes Tanganyika, Malawi and lately Albert, threatening their ecosystems and biota. The exploitation of hydrocarbon reserves is often portrayed as a unique opportunity to improve the living standards of the regional population; however the current situation in the West African Niger Delta dramatically illustrates why oil exploitation can also result in the demise of local economies, society and aquatic biodiversity. The process of extracting and transporting oil is complex, with possibilities for error and accidents that the African Great Lake region still lacks the infrastructures to clean up. An oil spill would therefore have direct and dramatic impact on the health, water supply and food security if not sustainably exploited and managed. Government of countries involved in exploitation should develop economically and ecologically viable strategies in collaboration with regional stakeholders and various scientists worldwide. Whatever the outcome of such consultations, it is imperative that environmental impact assessments are conducted by independent organizations to ensure that decisions on this matter are based on solid scientific assessments of the type and scope of environmental and societal damage including the breakout of national or ethnic conflicts that could ensue from an oil spill.