Aquatic filamentous fungi were surveyed from two brackish and two saline lakes in Egypt. Ninety-seven fungi (40 ascomycetes, 55 anamorphic fungi and 2 basidiomycetes) were identified from 764 fungal collections recorded from 545 samples collected from Lakes Edku, Marriott, Burullus and Quaron. Of these, 70 are new records for Egypt. This study represents the first report of aquatic fungi from the four lakes. Fungal communities in the four lakes were markedly different. Common fungi recorded at the four lakes were: Periconia prolifica (21.7%), Clavatospora bulbosa (12.8%), Cirrenalia basiminuta (12.7%), Panorbis viscosus (6%) and Ceriosporopsis halima (6%). Specious genera were: Cirrenalia (8 species), Phoma (8 species), Aniptodera (8 species), Achaetomium (6 species), Pleospora (4 species) and Zalerion (3 species). Higher fungal diversity was recorded from the two brackish lakes than those recorded from the saline lakes. In general, there was a decrease in fungal diversity with increasing salinity. Anamorphic fungi dominated the mycobiota at the four lakes and this is in harmony with the published data.