The alluvial plains of the two Somali perennial rivers, the Shebelle and Juba Rivers, have been and could be the breadbasket of Somalia. They have considerable potential for irrigation development. The civil war in the last two decades has however taken a severe toll on the institutions and infrastructure necessary to manage the water resources of the two rivers that is the lifeline of Southern Somalia. Flooding is now a frequent problem in the riverine areas and sometimes it takes the proportion of a catastrophic natural disaster, like in the 2006 Deyr rainy season. Natural flood plains have been encroached and the embankments have been cut to divert water during the dry season for irrigation purposes. The barrages and canals that were used to irrigate vast areas are now dysfunctional. Efforts are underway to prepare an integrated flood management plan and also to rehabilitate the irrigation facilities and revive the agricultural sector. These efforts are hampered by lack of knowledge of river basin behaviour in terms of hydrology, hydraulics, sedimentation, etc. and, lack of public institutions responsible for implementing sound river basin management measures.