Background: In most countries, cotton production is rainfed and relies on increasingly unpredictable rainfall patterns. The availability of water during plant development impacts productivity and fiber quality, and the development of plant ideotypes capable of maintaining their yield potential and adequate fiber quality under limited water supply is desirable. Tolerance to water stress depends on the complex interaction between mechanisms whose genetic bases are not well understood. This study aimed at characterizing plant growth parameters (biomass accumulation) in response to water stress of a panel of Upland cotton genotypes. Association studies allowed identifying markers associated with such a drought-tolerance related trait. Results: Two hundred and sixty nine cotton genotypes were grown under contrasting water regimes on PhenoArch, a High-Throughput Phenotyping Platform, and genotyped using 21.930 high-quality SNP markers. Water deficit affected biomass accumulation by 34% on average. High levels of genetic variability were observed (p<0.05) for biomass accumulation under both regimes, and heritability was moderate (46%). GxE interactions were of low magnitude. GWAS identified three (individually displaying an R2=10%) and five (individual R2=13%) markers for biomass accumulation, under water stress and control conditions, respectively, defined three and two genomic regions. None of the loci were common to both scenarios. Conclusions: While the analysis of the phenotypic data pointed out a lack of GxE interactions for biomass accumulation, GWAS uncovered distinct genomic regions. The genetic control of biomass accumulation appears to depend on environmental conditions. Once validated, these markers could prove useful for the marker-assisted selection of traits associated with tolerance to water deficit.