With their sources in the Ethiopian highlands, these rivers flow in a generally southerly direction, cutting wide valleys in the Somali Plateau as it descends toward the sea; the plateau's elevation falls off rapidly in this area. The adjacent coastal zone, which includes the lower reaches of the rivers and extends from the Mudug Plain to the Kenyan border, averages 180 meters above sea level.

The Jubba River enters the Indian Ocean at Kismaayo. Although the Shabeelle River at one time apparently also reached the sea near Merca, its course is thought to have changed in prehistoric times. The Shabeelle now turns southwestward near Balcad (about thirty kilometers north of Mogadishu) and parallels the coast for more than eighty-five kilometers. The river is perennial only to a point southwest of Mogadishu; thereafter it consists of swampy areas and dry reaches and is finally lost in the sand east of Jilib, not far from the Jubba River. During the flood seasons, the Shabeelle River may fill its bed to a point near Jilib and occasionally may even break through to the Jubba River farther south. Favorable rainfall and soil conditions make the entire riverine region a fertile agricultural area and the center of the country's largest sedentary population.