Pollution of the environment with heavy metals is a serious problem that is recognized in most countries in the world. Lake Timsah as an important lake in Suez Canal is highly polluted and receiving different sources of contaminations. However, attention and alarm thresholds of these parameters only concern the toxic effects of the polluting substances studied and do not take into consideration the question of chronic exposure at low doses of noxious chemicals. The physico-chemical parameters only provide snapshots of the condition of a water body and don't provide the integrative measure of overall health of any water body. On the other hand, crustaceans are used as bio-indicators in various aquatic systems in bio-accumulation experiments and in field studies. The crustacean isopod, Sphaeroma serratum which is found in large numbers at Lake Timsah was used for further investigation for detecting its DNA damages cause by the pollution. The comet assay technique which derives its name from the comet-like shape that cells with damaged DNA acquire was applied in this study in order to investigate on what level such poor water conditions in Lake Timsah can deform the DNA of its biota. It is recommended than other tests as it requires only a very small number of cells and these cells do not need to be undergoing active division. The present study confirmed the applicability of the alkaline comet assay technique as a sensitive tool for environmental monitoring. Also, it can be suggested that aquatic S. serratum which is a very tolerant species can resist pollution and can be used as a reliable bio-indicator of DNA damage.