MicroRNAs (miRNAs) are critical regulators of gene expression that play multiple functional roles in plant abiotic stress responses. The durum miRNA transcriptome, target transcriptome and their roles in water deficit stress adaptation are poorly characterised. This study revealed that durum miRNA/target regulatory modules could contribute to genotypic water stress tolerance capacity across different durum varieties. Illumina sequencing of 96 small RNA libraries characterised 69 conserved and four novel stress-responsive miRNAs, of which several miRNAs showed inverted regulatory profiles between stress-tolerant and -sensitive genotypes. Genome-wide in silico analysis using an updated Triticum transcriptome assembly identified over 1000 targets for stress-responsive durum miRNAs, including proteins that play critical roles in stress signalling and metabolic processes. qPCR profiling confirmed 50 targets and 12 miRNAs with stress- and/or genotype-associated differential expression, while 5′RACE successfully validated that nine mRNA targets were cleaved by stress responsive miRNAs. The miR160/Auxin Response Factor module is currently being studied in detail. Overall, this study provides valuable insights into deciphering the miRNA-mediated molecular network underlying stress tolerance in durum wheat.