The long term monitoring of aquatic ecosystems based on chemical analysis is expensive resulting in a lack of time series data for management purposes thus necessitating the need for new cost effective methodologies. This study developed a fish-based index of biotic integrity (FIBI) for monitoring environmental conditions in riverine ecosystems within the Lake Victoria Basin, Kenya. The fish fauna in the basin is poorly studied, less diverse and ecologically specialized than the temperate fauna that provided the origins of the Index of Biotic Integrity. Fish samples were collected by electrofishing from 24 sites during baseflow periods in February, March and July 2004. Validation data were collected from 7 sites with varying levels of degradation. Fish samples were identified, counted and grouped into different trophic groups, relative tolerance to pollution, habitat guild and whether exotic or native to riverine environment. Thirty-three candidate metrics were evaluated for responsiveness to habitat quality and twelve were selected for inclusion in the final index. The index classified 6 of the 7 validation sites according to their levels of degradation. As a bioassessment tool, the index was useful in laying the basis for long-term monitoring of rivers in the Lake Victoria drainage basin. Copyright © 2010 John Wiley & Sons, Ltd.