A multidisciplinary study analyzed the degradation of the habitats of Lake Tanganyika on the coast of Burundi. Several river mouths and the lake shore were sampled near the city of Bujumbura and in the southern part of the country for analysis at several levels: physical chemistry, diatoms, macrophytes, macrophytes, macroinvertebrates and fish. The results obtained on the basis of these indicators demonstrate that the Kanyosha River has more potential in terms of ecological quality, while the Muha River and Ntahangwa seem to be the most polluted. Biodiversity is richer in the south (especially the Kamango, Murembwe and Rwaba tributaries). In addition to the typology of the sites sampled, all the evidence shows a general deterioration of tributaries in the coastal environment, and more accentuated in the north of the lake, around Bujumbura. This study aims to alarm the scientific community and decision-makers about the gradual degradation of the lake, and to express the need to set up a monitoring system on the dynamics of biodiversity and the quality of the water of Lake Tanganyika based on the study of bio-indicators as a basis for decision and management in order to mitigate and stop the pollution and the alarming degradation of the Lake.