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Riverine ecosystems are continuously been compromised by human activities resulting in threatening their integrity. In this study, integrity of Upper Victoria Nile River was assessed using habitat quality and fish biotic indices. Experimental gillnetting was done bi-annually in 9 stations along the river from 2008 to 2018. Nine habitat metrics were used to estimate habitat quality index at every sampling station. Fish sampled, were sorted, identified to species level, and weighed. Counts of introduced and indigenous as well as tolerant and intolerant species were recorded to generate species richness. A total of 10.642 fish, 65 species belonging to nine families were recorded. Dominant species were Lates niloticus 62.79%, Oreochromis niloticus 23.51%, Mormyrus kannume 13.64%; other species were ≤0.06%. Tolerance and trophic guild showed carnivores (61.5%), omnivores (21.5%) and detrivores (16.9%).Mean habitat quality index, total fish catch and fish-based index of biotic integrity varied among stations with highest record of 26.6±6.9, 289.2±51.8 and 30.6±7.9 at sampling station (ST4) respectively. The lowest was 19.4±7.3, 93.1±13.2 and 26.7±6.8 at sampling station (ST2) respectively. On a spatial basis, indices recorded significant differences among stations (p < 0.05). Results indicated a fair fisheries biodiversity that need better conservation management of habitat type of the upper Nile.