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Benthic algae and macroinvertebrates play important role in global functioning of aquatic food web. Their spatial and temporal distributions in relation to environmental variables and fish composition were the aims of this study. Both benthic groups of organisms were studied at 10 sites covering the whole area of Lake Qarun. Total of 164 algae species belonging to phyla: Cyanobacteria, Bacillariophyta, Miozoa (previously Dinophyta), Chlorophyta, Cryptophyta, Ochrophyta and Euglenozoa (previously Euglenophyta) were recorded. Macroinvertebrates communities consisted of 16 species representing phyla: Arthropoda, Annelida and Mollusca. The highest densities of benthic algae and macroinvertebrates were recorded in the middle sub-region of the lake in line with the co-domination of tilapias, mullets, soles and anchovy, whereas their lowest density at site 1 in the eastern area. The sites primarily located in the western sub-region with higher density of benthic organisms and domination of Mugil cephalus were distinctly separated from the other sites. Similar trend was in distribution of chlorophyll a content, which strongly correlated with density of benthic algae. Temporal distribution indicated higher algae density in spring and summer, and higher macroinvertebrates density in spring and autumn. The fish community’composition was spatially and temporally different and environmental variables were more similarly distributed.