The primary objective of the present work described in this manuscript was to develop some understanding of improving water stress tolerance in upland cotton through selection and breeding. Root is an important plant organ related to drought stress and significant achievements have been obtained, using rooting technique, for other stresses e.g. salinity. To achieve the objective, 80 cotton accessions were screened out measuring four morphological plant characters including root length, and one physiological parameter i.e. cell membrane injury. Water stress imposed for 45 days significantly reduced shoot length, root length, shoot fresh weight and shoot dry weight of 80 cotton accessions, and these accessions differed to a great extent from each other, and sensitivity varied from very tolerant to very sensitive. Some of the accessions like B-557 and DPL-26 showed small leakage of ions due to stress, and were revealed as moisture stress tolerant accessions. Cell membrane injury showed a positive relationship with moisture stress tolerance. The injury was less in tolerant accessions, thus it proved to be a reliable indicator of water status. Indices of stress tolerance showed a wide range of variability based upon parameters measured. The genetic basis of variation in moisture stress tolerance was investigated using the diallel technique. Both additive and dominance properties of genes appeared to control variation at low and high moisture stress, but genes acting cumulatively were more associated with the stress phenomenon. Due to the additive gene effects, estimates of narrow sense heritabilities for water stress tolerance were greater, showing that rapid improvement in the character may be made through single plant selection from F2 segregating population, based upon final productivity of seed cotton yield. Physiological mechanisms like cell membrane injury, relative water content and excised leaf water loss are also conditioned by polygenes, and thus may be improved through selection. The overall conclusion of this work is that cotton varies for moisture stress tolerance, and this tolerance has a reasonably good additive component, and further breeding work would be valuable for developing upland cotton cultivars suitable for moisture deficit area.