River Nile represents the most important source of freshwater in Egypt. There are several factors lead to the water pollution in the River Nile System (main stream Nile, drains and canals). The water quality of River Nile was good despite high organic loads discharged from some of the drains and industrial activities. These were harmful both to human and stream ecosystem health. A biological approach to monitoring water quality incorporates use of stream organisms themselves as a basis for pollution detection. Fish and aquatic insects considered as bio-indicators of pollutant effects and help to investigate possible environmental problems. One of the recent biochemical techniques for detecting DNA damage as a result of DNA single strand breaks, alkali-labile sites, and cross-linking is the alkaline (pH>13) single cell gel SCG assay. In this study the comet assay measure the DNA damage in various stages of the mosquito Culex pipiens collected from two different polluted water streams (Nikla and Elmansoreyh). The DNA damage measured in 3 rd , 4 th larval instars, pupa, male and female adults. It is clear from the results obtained in this study that the genotoxicity of water pollution of two different polluted water streams (Nikla and Elmansoreyh) in C. pipiens was high in larval and pupal stages and this study affirmed the appropriateness of the comet assay as a sensitive tool for environmental monitoring. Additionally, it can be proposed that C. pipiens is a strong aquatic bioindicator of genotoxicity.