MULTIPLE biomarker systems have been frequently used to measure the genotoxic effects of environmental pollutants on living organisms. In this study, faba bean seedlings were used (Vicia faba) as a bioindicator for water pollution. Five different sources of water: distilled water as a negative control, tap water, and polluted water from three different sources were used in irrigation of bean plants. All treatments showed great alterations in seed proteins, isozyme systems (α- esterase, β- esterase, peroxidase, and acid phosphatase) and DNA polymorphism detected by RAPD analysis. The detected variations between treatments included alterations in number (appearance and disappearance), staining intensity, thickness and relative mobility of bands. These results suggest that the irrigation by wastewater can cause genotoxic effects on plant and V. faba can be used as a bioindicator for evaluation of environmental pollution.