The water resources of the Juba and Shabelle rivers in southern Somalia are important for irrigation and food production, but are influenced by seasonal floods. Prior to the outbreak of civil war in 1991, the Somali Ministry of Agriculture successfully operated a hydrometric network covering the Juba and the Shabelle, data from which provided input to a flow forecasting model. The war resulted in the neglect and abandonment of monitoring stations and an enforced cessation of data collection and management. In 2001 and 2002, part of the pre-war hydrometric network was reinstated and water levels were again recorded at some stations. This paper examines the implications of the 11-year hiatus in data collection, and the now much reduced monitoring network, for assessing and managing the surface water resources. The problems faced have relevance to other basins, within Africa and elsewhere, where there has been a similar decline in data collection.