Ducrosia anethifolia Boiss is a medicinal and aromatic plant that is used as a food additive and drug in the areas of natural distribution. In this study, eight populations from different geographical regions of Iran were evaluated for their essential oil composition, total phenolics and flavonoids as well as for free radical scavenging activity during two consecutive years under water deficit. Analysis of variance was performed using a randomized block design at three levels of irrigation and 2 years, using the GLM procedure of SAS software and cluster analysis was used according to Ward's method using squared Euclidean dissimilarity. The highest essential oil and total phenolics/flavonoids content were obtained in the second year. GC–MS analysis was used to analyze the essential oil components. In normal conditions, cis-chrysanthenyl acetate (39.1–66.4%) and α-pinene (1.02–4.7%) were recognized as major compounds. The essential oil components were elevated under water stress. The highest increase in cis-chrysanthenyl acetate (21.32%) in response to water stress was observed in Abarkuh1. Elevation in total phenolic, flavonoid and antioxidant activity was also observed in plants subjected to water deficit. The highest content of phenolic acids was measured in Semirom (136.74 mg TAE/g DW), while the highest flavonoid content was in Kerman (6.05 mg QUE/g DW) in severe water stress condition. Finally, a high diversity in the studied populations can be used to select advantageous populations for other pharmaceutical and food purposes.