Floods are a common phenomenon in the riverine areas of the Juba and Shabelle River basin. The two rivers exhibit seasonal characteristics in their hydrological regime with high tendency of flooding especially during the Deyr (October to November) rain season. Some of the major flood events in the two basins in the past few decades occurred in the years 1961, 1977, 1981, 1997 and 2006. The floods are mainly caused by high rains experienced on the upper catchments of the two rivers in the Ethiopian highlands. However, the contribution of human activities to the floods is also significant, with the riparian farmers cutting the river banks to allow water flow into their fields during low flows. These illegal activities have increased after collapse of the central government in 1991 and exacerbated by El Nino 1997/98 rains that contributed to further destruction of the irrigation and flood control infrastructure.