Two Lyzimeter experiments were conducted at Sakha Agricultural Research Station, Kafr El-Sheikh Governorate Egypt, for two seasons, 2010/2011 and 2011/2012 Lyzimeters (100 x 70 x 90 cm) were filled with clayey soil and irrigated with for three water treatments twenty five years The present study aimed to investigate the effect of irrigation water quality for long-term on productivity of three onion cultivars Behairy Red (CV₁), Giza 20 (CV₂) and Giza Red (CV₃). Three irrigation water qualities; Nile water (W₁), agriculture drainage water (W₃) and mixed water; W₂ ( 50% W₁ + 50% W₃) used for irrigation to study its effects on onion contents from four heavy metals Ni, Cd, Pb and Cu and some soil characteristics. A split–plot design with four replicates was used where, water treatments and cultivars were allocated to main and sub-plots, respectively. The obtained results showed that: Using poor water quality for irrigation increased ECe, SAR, soluble cations and anions in soil paste extract and DTPA extractable heavy metals in soils (Cu, Ni, Cd and Pb) than that of mixed or good water quality. The maximum values of marketable yield and total bulbs yield/fed. As well as bulb quality (bulb diameter and average bulb weight) were obtained by irrigated with Nile water, while the lowest values were obtained by agriculture drainage water in 1^st and 2^nd seasons. Behairy Red cultivar produced the highly significant marketable yield and total yield, and significantly decreased culls yield as well as bulb quality (bulb diameter and average bulb weight). On the other hand, Giza 20 produced the highly significant total soluble solids (TSS%) in both seasons. The highest values concerning the previous characters were obtained with Behairy Red cultivar under Nile water irrigation, whereas the lowest values were obtained by Giza Red in soil irrigated with agriculture drainage water in both seasons. Content of the studied heavy metals were greater in bulb than in leaves. The results showed that Behairy Red cultivar (cv₁) was more tolerant cultivar to agriculture drainage and mixed water and its contents of Ni, Pb and Cu. No significant differences were found between Cd content at all studied onion cultivars used for. The heavy metals content of onion cultivars from can be arranged as follows:                         With Pb: CV₁3 < CV₂                         With Cu: CV₁ < CV₂ < CV₃                         With Ni:  CV₂ < CV₁ < CV₃