The Lake Chad basin is one of the most unstable regions in Africa. The lake itself has shrunk and nowadays it covers less than 10 % of its area in 1960. These environmental changes have wider geopolitical consequences in the whole region, which encompasses countries such as Nigeria, Niger, Chad and Cameroon. Therefore, it seems that environmental threats may act as the detonators for larger political conflict as well as for a struggle for land and may cause growing instability in affected countries. The region is fragile, owing to the fact that several terrorist and Islamist groups are operating there. The most serious threat in the Lake Chad basin is militant Islamist group Boko Haram, which is based in north eastern Nigeria, but it is also active in neighbouring countries. As a result of both ecological changes and security threats, people are losing their traditional sources of income from herding and it is likely that there will be large waves of migration from the area. The paper focuses on the environmental challenges in the Lake Chad basin and their effect on the security in the region. The main attention will be paid to the strategies and actions of militant terrorist groups such as Boko Haram that will be analysed in the wider regional geopolitical context.