Lake Qarun, one of largest and oldest lakes in Egypt, was declared as a nature reserve in 1989 to protect the biological, archaeological, and geological diversity. However, Lake Qarun is bearing a load due to various pollution types. This condition has resulted in unfavorable water. There is a greater combination between water pollution and health problem. For the protection of lake all waste waters should be managed and remediated appropriately. Bioremediation has been recognized to be environmently friendly and economical for treating the pollution of water bodies. Bioremediation uses naturally occurring bacteria, fungi, or plants for degradation or detoxification of harmful substances. Integration between nanomaterials and bioremediation has great potential to be effective and efficient. Therefore, myco-remediation using silver nanoparticles was chosen in this study. Ecological modelling using MIKE 21/3 was used for completion of the evaluation of lake water quality, bioremediation process, and to simulate the transport and fate of pollutants in the lake.