The current study aimed to explore the biodiversity of water-borne spora of Ingoldian mycobiota from mixed submerged plant litter and surface water of two water areas at Assiut (Upper Egypt). Thirty-eight identified species in addition to three unidentified species and fifteen unknown fungal taxa related to twenty-five fungal genera were gathered from either submerged mixed plant litter or surface water samples collected from twenty water sites at Nile River and El-Ibrahimia canal at Assiut (10 sites for each). Of these fungi, twenty-one identified species, two isolates were identified on only genus level in addition to 14 unknown fungal taxa are new records for Egypt. The samples collected from the Nile River were the richest and highest diversity (38 identified species, 3 unidentified species which belong to 25 genera in addition to 14 unknown taxa) in comparison with those collected from the El-Ibrahimia canal (19 identified species and one unknown taxon which belong to 7 genera only). The fungal taxa were isolated from water samples using Ficus leaves as substrates (baits). The monitored Ingoldian fungi varied in their occurrence frequency, diversity and abundance depending upon the sampling source and the employed substrate. Anguillospora, Dactylella, Triscelophorus, Flagellospora and Lemonniera were the most prevalent fungal genera. Anguillospora longissima, A. rosea, Dactyllela arnaudi and Triscelophorus monosporus were the commonest species. The broadest species spectra were recorded for Dactylella (6 species), Anguillospora (4 species), Lemonniera, Pyramidospora and Triscelophorus (3 species for each). The samples collected from the Nile River exhibited a higher fungal diversity and abundance than those collected from the El-Ibrahimia canal. Twenty-five species related to 18 fungal genera in addition to 14 entirely unknown fungal taxa were exclusively recovered from the Nile River but completely missed in El-Ibrahimia Canal. All fungal genera and species gathered from the El-Ibrahimia canal, except one unknown taxon, were also represented in the samples collected from the Nile River. Most of the recovered fungi exhibited variable diversity, frequency of occurrence and abundance depending upon the sampling site, water body and substrate. This work provides a checklist, description and photos of some Ingoldian fungal taxa emerged from both experimented water bodies.