Seed water content affects wheat quality, storage, and food safety, influencing viability and fungal contamination risks. Grain moisture is influenced by both genetic and environmental factors, with agronomic practices aiming to optimize it. However, no genotype has been specifically developed for enhanced seed water properties, as the underlying biochemical and genetic mechanisms remain unclear. Using a durum wheat mutant (WM) with higher water affinity of leaves, compared to its wild-type cultivar, Trinakria (WT), this study investigates the biophysical and biochemical mechanisms affecting seed performance. Genotypic characterization of unaged seeds includes differential scanning calorimetry, metabolomic profiling, and functional analyses of water uptake rate, dehydration rate, and seed coat electrical resistance. Germination and Fusarium resistance were examined, too in both unaged and aged seeds. As for the leaves, WM seeds exhibit higher water-binding strength than WT. Metabolomic analysis revealed a higher polar/apolar ratio in WM (83 vs. 72 in WT), with significantly greater myo-inositol and raffinose content and lower levels of unsaturated fatty acids. No differences in seed imbibition velocity or dehydration velocity were observed, but WM showed lower seed coat electrical resistance, indicating greater free water retention on the seed surface. Under low Fusarium inoculum concentrations or in the absence of pathogens, aged WM seeds showed higher germination rates and vigor than WT. As an inherited trait, selecting for strong water-binding capacity, increased osmoprotective compounds, and lower unsaturated acid content could contribute sustainably improve seed longevity and Fusarium resistance.