In this study, screening of Artemisia dracunculus accessions was investigated under water deficit based on physiological and phytochemical traits. The results clearly indicated that water deficit significantly reduced the relative water content, chlorophyll, and carotenoid contents and increased malondialdehyde, electrolyte leakage, and antioxidant activities. The responses of tarragon accessions to water deficit, however, were inconsistent. The HPLC analysis revealed the presence of chlorogenic, syringic, ferulic, vanillic, chicoric, and p-coumaric acids as major phenolic acids, while quercetin and herniarin were detected as the predominant flavonoid and coumarin compounds in the extracts. Our findings revealed that the water deficit not only increased the amounts of herniarin, luteolin, apigenin, caffeic acid, and syringic acid, but also introduced quercetin that was not present under normal conditions in Estahbanat. Nevertheless, these results were highly impacted by the accession type. The results indicated that Hamadan, Varamin and Estahbanat accessions could be introduced as tolerant accessions. Given the very different responses of tarragon accessions to water deficit and the diversity between these accessions, the findings of the present study could be an effective step in identifying and achieving homogeneous, drought-tolerant and high-yield potential accessions, and may help tarragon breeding programs as well as development of cultivation.