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This paper examines the distribution of benthic macroinvertebrates in relation to physico-chemical conditions along 1 035km of the River Nile from Aswan High Dam to Al Kanater Barrage, Cairo. Total Dissolved Salts and several individual chemical variables showed positive linear regression with distance from Aswan. The creation of the Aswan High Dam has reduced the ionic concentrations discharged to the Nile, but there is a gradual increase as the river flows though Egypt. Benthic macroinvertebrates show overall low taxon richness with taxa typical of a lowland riverine region. Changes in taxon richness appear to be influenced by either pollution and/or sedimentation. Sites downstream of the Kema Factory and downstream of organic discharge from Etsa Drain from Minia city show severe pollution. A Bray-Curtis Diversity Index shows these sites to be biodiversity outliers consistent with the negative impact of pollution. Examination of 95% outlying chemical values confirms gross pollution from these sites and the data as a whole suggest other sites that may also be affected by pollution. A contributor to high macroinvertebrate taxon richness appeared to be increased sedimentation, particularly in midstream samples. It is concluded that the low ionic concentrations resulting from the Aswan High Dam construction, localised pollution, and the occurrence of sediment are the main factors governing macroinvertebrate taxon richness. These factors will require careful monitoring, assessment and management if the biodiversity of the Nile is to be conserved.