The African Rift Valley Lakes are freshwater; they are not brackish water. They all drain via rivers which are also freshwater (obviously). Example, Lake Tanganika, the largest and most alkaline of the rift valley lakes and the second deepest lake on the planet, is part of the Congo River basin and supplies the water to the Congo River via the Lukuga River. The Congo River is not brackish, it is absolutely completely freshwater containing no sodium salt.
There is a vast difference between "salt" as in brackish and sea water, and the "salts" that provide the alkalinity to the freshwater rift lakes.