Aquatic fungi from four brackish water lakes; Edku, Burullus and Manzala lakes which are located at the northern region of Egypt and Qarun lake that located in El-Fayoum city are reported in this manuscript. Twenty-nine fungal species which belong to 19 genera of aquatic fungi were recovered from water samples collected from the studied lakes. The most frequently isolated fungal species were Chytridium conferrop, Allomyces throughout and Rhizoclosmatium globosum. Thraustochytrium amoeboidum and Leptolegniella exoosporus have a moderately occurrence frequency. The maximum fungal count of recovered aquatic fungi was recorded in Burrullus lake followed by EdKu, Manzala and Qarun lakes. This study was extended to test the ability of six selected aquatic fungi(Brevilegniella keratinophila, Blastocladiella cystogena, Chytridium conferrop, Entophlyctis variabilis, Schizochytrium mangrovei and Thraustochytrium rosin), to uptake the radionuclide from their culture medium as a step to biologically treat the waste water or solution with radio-cesium and radio-cobalt. Fifty seven of Cs-137 and 35% of Co-60 could be removed from liquid waste by the selected aquatic fungi.