This study was conducted to analyze water quality from different resources using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to separate protein bands as a biomarker system for evaluating water quality. Onion roots were used as a bioindicator for testing water quality , in addition to different water resources included Nile water, agricultural drainage water from Khafr El- Sheikh Governorate and Menyet EL- Nasr center and industrial water effluents resulted from chemical fertilizer industry. All treatment of water demonstrated a great variations in the number of polymorphic bands such appearance and disappearance, staining intensity and relative electrophoretic mobility of bands. The Nile water treatment showed two specific bands which do not appeared in all of drainage water. The intensity of protein bands was decreased in high quality water from the Nile river in relation to other water resources which showed intensity response to less quality water. This indicated that intensity of protein bands was responded to less water quality. The maximum intensity was shown in the treatment with industrial drainage water. The results suggested that protein pattern separated by SDS – PAGE can be used a biomolecular marker for testing water quality. Therefore, protein profile seemed to be a suitable tool for screening water quality depending on the number of specific bands appeared in the treatment of high water quality which disappeared in less water quality. In addition to the intensity of bands which showed response to less water quality as seen in industrial wastewater which appeared more intensity of protein bands than other water resources tested in this study.