Randomly collected decaying leaves and senescent, dried leaf litter of Eucalyptus rostrata, Ficus nitida, Phoenix dactylifera, and Phragmites australis submerged for one year in the River Nile, small and large irrigation canals at Sohag, Egypt, were investigated for freshwater fungi. Thirty-six fungal species belonging to 33 genera were identified from 982 fungal collections recorded from 864 samples. The most common genera were Halobyssothecium represented by 221 records, Aspergillus (190), and Cylindrocladiella (102). Of the 36 taxa recorded, five are new to science, of which Robillarda sohagensis was previously described. Multivariate clustering analysis based on similarity between the 96 fungal communities has produced 13 groups. The type of collected samples; random or baited and the host are the important factors that influenced the fungal communities. Halobyssothecium unicellulare was collected from 59 communities followed by Aspergillus flavus (48) and Cylindrocladiella pseudohawaiiensis (32). The highest number of species and records was reported from randomly collected leaves of Phoenix dactylifera and Phragmites australis from both the River Nile and the small irrigation canal. Bartalinia robillardoides was reported for the first time from freshwater habitats in Egypt during the present study. A description and illustration of the Egyptian collection are provided. Phylogenetic analyses of the LSU rDNA sequence confirmed its identity.