In order to study the effect of water stress and micronutrients (Fe, Zn and Mn) on chlorophyll fluorescence, leaf chlorophyll content and sunflower nutrient uptake in Sistan region, a field experimental in split plot design with three replications was conducted in 2007. Alstar cultivar was comprised of water stress at two stages of growth (control, flowering and grain filling stage) as main plot and seven micronutrient foliar application treatments, Fe, Zn, Mn, Fe+Zn, Fe+Mn, Zn+Mn and Fe+Zn+Mn, as sub plots. Results showed, exertion of water stress in flowering and grain filling stage decreased grain yield of sunflower significantly. Use of foliar micronutrient increased grain yield in water stress; on the other hand, use of Mn foliar application had the highest positive effect on grain yield. Chlorophyll a fluorescence was increased under water stress at the two stages of growth. The highest chlorophyll a fluorescence was recorded in B-1 (foliar application of Fe), and maximum amount of chlorophyll content was observed in B-5 (foliar application of Fe+Mn). The highest seed contents of Fe and Mn were measured in the control treatment.