| Summary: | Streams and rivers are globally threatened ecosystems because of increasing levels of exploitation, habitat degradation and other anthropogenic pressures. In the Lake Victoria Basin (LVB) in East Africa, these threats are mostly caused by unsustainable land use; however, the monitoring of ecological integrity of river systems has been hampered by a lack of locally developed indices. This study assessed the health of four rivers (Nzoia, Nyando, Sondu–Miriu and Mara) on the Kenyan side of the LVB using physicochemical water quality parameters and a fish-based index of biotic integrity (IBI). Fish tolerance ranking was derived from principal component analysis of water quality parameters, and the concept of niche breadth (NB). The relationship between fish species and water quality parameters was examined with canonical correspondence analysis, whereas community metrics and stressors were evaluated through Pearson network correlation analysis. Fish species richness, trophic structures, taxonomic composition and species tolerance were used to generate the metrics for fish-based IBI. NB showed that most of the fish species were moderately tolerant to poor water. Moderately tolerant and intolerant fish species were negatively correlated with a high level of organic loading in the Mara River. Fish-based IBI scores for the rivers ranged from 26 to 34, with Sondu–Miriu scoring the lowest. Our results show that the cumulative effect of stressors can adequately rank fish species tolerance according to the disturbance gradients and further develop regional metrics to assess river health. Despite the fact that fish communities are declining, continual management and enforcement of environmental regulations are important, with conservation and management of headwaters and low-order streams being essential while they are still species rich.
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