To investigate the effect of draught stress on water relations, stomatal density, chlorophyll content and yield of rapeseed, an experiment was done with four levels of drought stress including L1 (Field Capacity, FC), L2 (70% Available Water Content, AWC), L3 (50% AWC), and L4 (30% AWC), within three growth stages- including stem elongation (T1), onset of flowering (T2) and silique formation period (T3) at the University of Maragheh in 2013. The results showed that the lowest relative water content and leaf water potential were obtained at 30% AWC and silique development stage. Meanwhile, the highest water use efficiency (WUE) was observed during flower bud and silique development stages and 70% AWC. Furthermore, the results demonstrated that stomatal was only influenced by the levels of applied stresses and the highest stomatal density was recorded in 30% AWC. Implementation of 30% AWC in silique development stage diminished chlorophylls a, b, and total chlorophyll content to their lowest points so that compared to field capacity (L1), they decreased about 59, 67 and 62 percent, respectively. Likewise, the least grain yield belonged to stress application at flower bud development stage and 30% AWC stress level. Also, the grain yield loss in L4×T3 (30%AWC in silique formation period) treatment in comparison with the L1 (Field Capacity, FC) was 46.2 percent. Seed protein content was adversely affected by stress level and any decrease in AWC led to a concomitant decrease in protein content. At the same time, seeds oil content was influenced by stress application times. Water deficit stress during flower bud formation had the greatest adverse effect on seeds oil content. Overall, it was concluded that severe water deficit (30% AWC) led to the decrease of chlorophylls a, b, total chlorophyll, seed protein, oil content and yield.