Microorganisms play a significant role in bioremediation of heavy metal contaminated soil and wastewater. The present study has been carried out to understand the tolerance potential of different species of Aspergillus (A. flavus, A. niger, A. nidulans, A. oryzae and A. terreus) which were isolated from the Nile water. The degree of tolerance of fungi was measured by minimum inhibitory concentration in the presence of different concentration of metals (Mn, Fe and Al) and compared to a control sample. Results showed variations in the tolerance level of different isolates of Aspergillus. A. niger and A. oryzae were tolerant while A. nidulans was the most sensitive species. Removal of manganese, iron, and aluminium using powder and viable Aspergillus oryzae biomass was investigated. Metals (Mn, Fe. and Al) removal increased with an increasing dose of biosorbent for the powder and viable biomass within two hours. These results showed that powder and viable Aspergillus oryzae biomass can be used for removal of heavy metals from polluted water.