A lyzimeter experiment was carried out at Sakha Agricultural Research Station, Kafr El-Sheikh governorate, Egypt, during two successive seasons 2011/2012 and 2012/2013. Lyzimeters (100 x 70 x 90 cm) were filled with clayey soil and irrigated with three water types since twenty seven years ago to study the effect of irrigation by different water qualities (fresh water, drainage water and blended water) on soil properties, productivity of flax varieties (Sakha1, Sakha2, Sakha 101, and Sakha 102) and their contents of heavy metals (Pb, Cd, Ni and Cu). The obtained results showed that, using poor quality water for irrigation increased ECe, soluble cations and anions in soil paste extract and DTPA extractable heavy metals (Cu, Ni, Cd and Pb) than that of blended or good water quality. Highl significant differences of yield and yield components among flax varieties were found due to irrigation water qualities and its contents of heavy metals. Heavy metals content was higher in the straw than that of seeds. No significant differences were found among Cd content for all studied flax varieties. No significant differences were found among Cu, Pb and Cd content in straw with all studied flax varieties. Cadmium content in studied flax varieties decreased as follows: Sakha 2 < Sakha 1< Sakha 101< Sakha 102, while the order was: Sakha 1 < Sakha 2 < Sakha 101< Sakha 102 for Pb, Cu and Ni. So, Sakha 1 was more tolerant variety to the irrigation with drainage and blended water