Drought stress can substantially affect growth and secondary metabolite production in medicinal plants. This study evaluated the growth, physiological responses, and phenolic compound contents of ten Thymus populations under greenhouse and field conditions with three irrigation levels: control, moderate stress, and severe stress (corresponding to 100%, 70% and 40%, respectively, of field capacity). Drought significantly reduced plant height, biomass, and relative water content, with T. serpyllum and T. daenensis-1 showing greater reductions in several growth and physiological traits. In contrast, T. kotschyanus-2 and T. vulgaris generally maintained relatively better growth and water status. Under stress, proline accumulation and electrolyte leakage increased, while photosynthetic pigments declined and carotenoid levels increased in several populations. Total phenolic and flavonoid contents generally increased under drought, particularly in T. vulgaris and T. kotschyanus-2. Rosmarinic acid, the predominant phenolic compound detected, increased significantly under drought stress. Essential oil content ranged from 0.33% to 2.50% across populations and environments and showed population-dependent responses to drought, with increases observed in several populations. Multivariate analyses and drought tolerance indices identified T. kotschyanus-2 as showing relatively better drought performance among the evaluated populations, based on its relatively smaller reductions in biomass, higher relative water content, and favorable biochemical responses. In contrast, T. serpyllum showed comparatively greater sensitivity to drought across several measured traits. Drought reduced growth while enhancing the accumulation of several phenolic and other specialized metabolites, suggesting a potential shift in resource allocation between growth and secondary metabolism. T. kotschyanus-2 showed relatively better drought performance, suggesting its potential for further evaluation under water-limited cultivation conditions. Comparison of the greenhouse and field experiments revealed common drought-response patterns as well as environment-dependent differences in their magnitude.