The fisheries of Lake Victoria in East Africa must be managed effectively to ensure sustainable food supplies. This has been impossible in the past due to inadequate knowledge of commercially important fish stocks. Here we present the first acoustic abundance estimates of fish in Lake Victoria. Five lakewide acoustic surveys were conducted between 1999 and 2001, using the Simrad EY500 echo-integrator with a 120 kHz split-beam transducer. There are many species of fish in Lake Victoria, however, only limited identification of targets can be achieved by present methods. Broad categories were distinguished by visual examination of echo-traces. The echo-integrals were partitioned between four target groups: (1) the Nile perch (Lates niloticus), a top predator, (2) small pelagics comprising mainly the dagaa Rastrineobola argentea together with mixed species of haplochromines, (3) the crustacean Caridina nilotica and (4) other species. Spatial and temporal differences in the Standing Crop were observed between north and south, and between shallow and deep water. Most fish were found inshore but the spatial distribution varied between seasons. Mid-lake fish densities were higher in August compared to February. In August, the water column is well mixed while in February it is stratified with a low-oxygen layer inhospitable to fish near the bottom. There are consequent changes in the characteristics of observed echo-traces. Over the survey series, Nile perch biomass showed a consistent decline, while the stocks of small pelagic species increased. We emphasize the need for simple rules to identify species, and hydrographic monitoring to assist echo-trace classification. In the absence of any other source of comprehensive biomass estimates, the value of acoustic surveying in Lake Victoria is demonstrated.