Treated wastewater could be considered as a new water resource in agriculture especially in arid and semi-arid regions of the world such as Iran. Two one-year field experiments were carried out to determine the effects of municipal treated wastewater on yield and seed heavy metals content of sunflower cultivars, in Research Farm of Yazd Municipal Wastewater Purification Station during 2015 and 2016. The climate of the region was hot and dry according to Koppen climate classification system. Experiment was arranged as split plot based on randomized complete block design with three replicates. Treatments were three irrigation water types as main plot consisted ("WW": irrigation with treated municipal wastewater thoroughly, "WW/FW": irrigation with treated wastewater/fresh water alternatively and "FW": irrigation with fresh water thoroughly) and three sunflower cultivars (Azargol, Record, and Farrokh) as subplots. The following parameters were assessed: plant height (cm), head diameter (cm), seed numbers per head, unfilled seeds per head, seed and biological yield (kg/ha) and seed heavy metals content. Results showed that the highest plant height (194 cm) obtained in Record and the highest head diameter (21.5 cm) obtained in Farrokh cultivars, which were irrigated by WW. Treated municipal wastewater also increased seed yield by 10.7% compared to FW treatment. The highest (5029 Kg/ha) and lowest (3734 Kg/ha) seed yield were obtained in Azargol and Farrokh that irrigated with WW and WW/FW treatment, respectively. However, application of treated municipal wastewater lead to accumulation of trace elements (Fe, Mn, Zn, Cu, Cd, Pb, and As) in seeds; but, the values of all the elements were below the permissible limits recommended by World Health Organization. It is concluded that WW could be used for irrigating sunflower crop without worrying about the accumulation of toxic substances.