Plant uptake is one of the major pathways by which toxic metals enter to human food chain. The irrigation water, important source of toxic metals, is contaminated with effluent and other pollutants due to the widespread industrialization. Two lyzimeter experiments were conducted at Sakha Agric. Res. Station, Kafr El-sheikh, Egypt, for two successive seasons, 2010 and 2011.It aimed to study the effect of irrigation water quality for long –term on productivity of four cotton genotypes; Giza86, Giza87, Giza88 and Giza89 in the two seasons were to study the content of their root, stem, leaves, and seed cotton of heavy metals; Cd, Ni and Pb as affected by irrigation water quality. Lyzimeters (100\ 70/ 90 cm) were filled with clayey soil was irrigated with three water qualities since 1987. They were _W1, Nile water, W₃, drainage water and W₂, mixed water, 50% W₁+50%W₃. A split –plot design with four replicates were used where, irrigation water quality and cotton genotype were allocated to main and sub-plots, respectively .The obtained results showed that using drainage water quality for irrigation increased ECe, SAR, soluble Na⁺, Mg⁺⁺, So4⁼and Cl^- in soil paste extract, total and available Pb,Cd and Ni than that of mixed or Nile water. The results show also that the effect of genotypes were different significantly for all studied cotton yield and same characters of tested genotypes .The effect of drainage water on studied genotypes were significantly different on most studied characters; the highest values for seed cotton yield , seed and plant high were obtained from Nile water followed by mixed water mean while drainage water gave the lowest values for this characters .The interaction between water qualities and cotton genotypes were significant in some studied characters. In general, stem cotton of the studied heavy metals were higher than that of root, leaves, and seed cotton for all water quality treatments .Cotton root, stem, leaves, and seed cotton contents of Pb ,Cd and Ni greater when drainage water ( W₃ ) was applied than that of the mixed or Nile water.