Cotton production in Mediterranean environments is increasingly constrained by water scarcity, affecting both yield and fibre quality. This study evaluated the response of two cotton species, Gossypium hirsutum Cav. (upland) and Gossypium barbadense L. (Pima) to full and deficit irrigation. A field experiment with two factors {irrigation level [full (C) - 600 mm and reduced (D) - 450 mm] and genotype [G. hirsutum (U) and G. barbadense (P)]} and 3 replicates was laid out at the Agricultural University of Athens. Crop and lint yields, fibre quality traits and anatomical characteristics (upper half mean length (UHML), uniformity index (UI), short fibre index (SF), micronaire (Mic), maturity (Mat), elongation (Elg), strength (Str), reflectance (Rd), yellowness (+b), trash content (TrCnt), trash area (TrAr) and spinning consistency index (SCI)) were measured. Deficit irrigation reduced yield, particularly in upland cotton, with reductions approaching 39 %. Pima cotton exhibited higher uniformity (4 %), Str (40 %) and SCI (53 %), while upland cotton showed higher Elg (11 %) and Rd (5 %). Water deficit increased Mic in upland cotton and reduced fibre Str and spinning performance in both species, with more pronounced effects in Pima. Anatomical analyses revealed thinner fibres in Pima and increased convolution density under drought. Overall, genotype exerted a stronger influence on fibre quality than irrigation level, whereas yield was more sensitive to water limitation. These findings highlight the importance of species selection to sustain fibre quality under limited water availability and the use of Pima for improved textile performance in water-stressed environments.