A study of the floristic biodiversity of the areas bordering the lakes of northern Burundi was carried out in three stations respectively: the coastal lake zone, the swampy coastal part and the mainland. The results highlight indicators of the deterioration of the ecological qualities of lakes in northern Burundi. We cite the development of vegetation of invasive species such as Lantana camara on the small island of Lake Rwihinda, the establishment of Eichornea crassipes on Lake Rweru, and the development of a floating carpet of Nymphaea lotus and Nymphaea caerulea. Restorative action by greening the banks by giving priority to species native to the Bugesera region is to be undertaken.