The fine regulation of root and stomatal architecture and physiological responses in crop plants towards drought stress is reported in the present study. The impact of water stress on relative water content (RWC), chlorophyll content, stomatal index and plant growth traits were evaluated in the two contrasting cotton varieties i.e., LRA-5166 (drought-tolerant) and NBRI-67 (drought-sensitive) during water stress. Results exhibited the significant variation in RWC, root and shoot length, root dry weight as well as an alteration in stomatal index between LRA-5166 and NBRI-67 subjected to water stress. Under water stress shoot dry weight, total dry weight and chlorophyll content in LRA-5166 were not found altered while it reduced in NBRI-67. Collectively, we demonstrated the two varieties of cotton behave differently to maintain biomass and withstand water stress. Moreover, we suggested that the physiological roles of increased root growth with reduced stomatal index distinctly maintain water homeostasis in LRA-5166 and NBRI-67 under water stress. These studies collectively demonstrated that phenotypic plasticity of root and stomata could play a significant role in regulating the biomass productivity and stress-tolerant in cotton during drought.