As the second deepest lake in Africa, Lake Tanganyika plays an important role in supplying fish protein for citizens in the catchment. However, the lake is increasingly threatened by environmental pollution with the development of social economy and expanding of population. In order to reveal the external source of heavy metals in Lake Tanganyika, 16 surface sediment samples from the rivers which flow into the northeast of the lake were collected and analyzed. Besides the contents, the potential ecological risk indices (RI) of each heavy metal were also analyzed. Furthermore, the relationship, between land use and the spatial distribution of heavy metals was also discussed. The average contents of Cu, Zn, Cd, Pb and Hg were 18. 4, 21.2, 0.05, 6.6 mg x kg(-1) and 8.4 ng x g(-1), respectively, with the maximum values of Zn, Pb and Cd located in Bujumbura urban rivers. The data indicated that all the inflow rivers were at low potential ecological risk. RI of heavy metals ranked as the following order: Cd > Hg > Cu > Pb > Zn, as Cd being the key element contributing to the risk. The relationship between land use and heavy metals showed that the contents of heavy metals were highest in urban areas, followed by estuarine wetlands, and woodlands were least polluted by heavy metals. This distribution type implied that human activities could cause the heavy metal accumulation in the surface sediments of nearby rivers. The urban areas and estuarine wetlands need to be concerned in the further study.