The ecology of Lake Victoria and rivers draining its 180 000 km2 basin has changed over the past century in response to growing anthropogenic influences that have altered basal resources, trophic status and interactions and river flow regimes. Impacts on the ecology of the lake are well known, but little attention has focused on the ecological status of rivers supplying ecological services to the majority of the basin’s over 30 million inhabitants. In this paper, we review existing research on the ecological status of streams and rivers in the Lake Victoria Basin (LVB) and evaluate how they fit into emerging models of riverine ecosystem function in the tropics. Studies to date indicate that allochthonous sources dominate inputs to food webs in forested headwaters and savanna mid-reaches of rivers in the LVB, although transfer pathways vary with position in the river. Although riparian vegetation phenology and hydrologic run-off pathways control the spatial and temporal fluxes of energy inputs in headwater streams; animals play increasingly important roles in savanna mid-reaches. Over the last half century, food web studies have revealed widespread omnivory and a tendency toward increased omnivory among fishes whose diets were more specialized prior to the introduction of Lates niloticus and the ecological changes in the lake. Ecological patterns and processes in LVB rivers generally fit emerging models for the tropics, but studies completed to-date do not find autotrophic energy sources to be important. The findings of this review highlight the importance of specific management actions and needs for future research. Copyright © 2012 John Wiley & Sons, Ltd.