Nowadays natural water resources are being polluted with heavy metals that became very common issue in the country as well as all over the world as a result of increase in anthropogenic activities that leads to excess heavy metals' release like Copper, Mercury, Lead, Nickel and Zinc to alarming level which may significantly affects human and other living organisms as well so, there have to be treatment of waste water. Reports revealed that biological treatment, especially by using filamentous fungi that have a significant part in removal of heavy metals from the contaminated water. Hence in the following study we have isolated filamentous fungi such as Trichoderma sp., Aspergillus niger, Mucor sp., Penicillium sp. and Fusarium sp. from Oxidation Ponds of Sadat City that have been exposed to heavy metal contamination with aim to find their tolerance properties towards selective heavy metal metals like, Copper and Mercury. Findings of our study highlighted that Trichoderma sp. have greater ability to grow under varying Copper and Mercury concentration and shows greater tolerance limit of 37.67mm (Diameter of fungal species) at 200 mg/L of Copper concentration and tolerance limits of 29.67 mm (Diameter of fungal species) at 200 mg/L of Mercury concentration. Thus, it is concluded that the filamentous fungi namely Trichoderma sp., Aspergillus niger, Mucor sp., Penicillium sp. and Fusarium sp. are efficient in removal of toxic heavy metals from the poluted water. Hence, we can employ these fungi individually or in consortium as effective agents for bioremediation of the contaminated water in order to enhance the amount of clean water and increase the yield of useful crop plants for supplying the demand of growing population.