The waters of the Kagera are thus provided by two major tributaries, the Nyabarongo of Rwanda, which feeds Lake Rweru, and the Ruvubu of Burundi.

In 1894, German Gustav Adolf von Götzen crossed the Kagera at Rusumo Falls, marking the Rwandan colonial era that officially started in 1899.

[5] Additionally, there are at least 15 undescribed species of haplochromine cichlids that are endemic to some of the lakes in the upper parts of the river basin.

[6] Because of the many waterfalls and rapids, the various sections of the Kagera River basin are clearly separated, making movements by fish between them difficult or even impossible.

[5][7] During the Rwandan genocide of 1994, the Kagera was used to dispose of corpses as thousands of Tutsis and Hutu political moderates were murdered on the river banks.