Introduction Soil salinity poses a persistent constraint on agricultural productivity in arid and semi-arid irrigated regions, particularly for sensitive high-value crops such as fine-staple cotton (Gossypium barbadense L.). Addressing this challenge requires integrated agronomic strategies that simultaneously sustain yield, improve water-use efficiency, and protect soil-water resources under saline field conditions. Methods This study evaluated a Sustainable Intensification (SI) strategy for G. barbadense production in the saline-prone meadow-takir soils of the Surkhandarya region, Uzbekistan. In a two-year split-split-plot field experiment (2024-2025), we investigated the main and interactive effects of two genotypes (SP-1607 and Termiz-202), two irrigation regimes (70-75-65% vs. 70-80-75% of Field Capacity, FC), and three planting configurations (60 cm single-row; 76 and 90 cm twin-row) on seed cotton yield, water-use efficiency (WUE), soil porosity, and total dissolved solids (TDS) dynamics in the 0-100 cm profile. The 2024 and 2025 growing seasons were characterized by a semi-arid continental climate, with mean temperatures during the vegetative period of 27.6 degrees C in both years and low growing-season precipitation (23.8 mm in 2024 and 31.8 mm in 2025), indicating that irrigation management was the dominant factor controlling root-zone moisture and salinity. Results The SP-1607 variety under the intensified 70-80-75% FC regime combined with the 90 cm twin-row configuration (150-160 thousand plants ha(-1)) produced the highest seed cotton yield (4.82 t ha(-1); +32.4% vs. control, p < 0.05) and the highest WUE (1.39 kg m(-3); +25.2%). Seasonal water inputs remained within 3,236-3,452 m(3) ha(-1) across configurations, reducing water input per ton of fiber by 20.6%. Under the intensified regime, profile TDS declined from 1.232% to 1.090%, compared with 1.232% to 1.185% under conventional management, suggesting a more favourable short-term salt balance in the root zone. Soil porosity decline was smaller under the intensified package (-1.5 percentage points) than under conventional management (-2.2 percentage points). Discussion These site-specific findings from a two-year, single-location trial indicate that the combination of an intensified irrigation threshold, a salt-tolerant genotype, and a high-density planting configuration can concurrently improve yield, water productivity, and short-term soil structural stability in weakly saline meadow-takir soils; however, multi-location and longer-term validation is required before broader recommendations can be made.