To study the effect of water stress on some physiological characteristics, an experiment was carried out in a simple lattice design with two replications under normal and low irrigated conditions using 49 cumin endemic ecotypes collected from different parts of Iran in the crop year 2011-2012 in college of Aburaihan, University of Tehran. Physiological traits including content of proline, soluble sugars, essential oil, chlorophyll a, chlorophyll b, carotenoids and relative water content were measured beside grain yield. The results showed significant effect of drought stress on all the traits. Drought stress decreased chlorophyll a, b and carotenoids content, grain yield and relative water content about 40, 32, 52, 19 and 9 percent, respectively. Meanwhile, contents of proline, soluble sugars and essential oils increased about 30, 55 and 56 percent, respectively. According to the results of mean comparisons, ecotypes of Kashmar, Chatrood, Ivanaki, Gonbad, Ardekan, Sivand, Qaen and Baneh had the high amount of carotenoids, chlorophyll a, chlorophyll b, relative water content, soluble sugars, proline, essential oil content and grain yield, respectively. In general, cumin as a moderately tolerant plant to water deficit exploit different physiological mechanisms to cope with stress and breeding strategies focusing on physiological aspects can be applied to improve high yield cultivars tolerant to drought stress.