Intertidal ectotherms live at their physiological limits, where minor environmental shifts could be instantly reflected in the species physiology, population fitness and community dynamics. In the present study, we quantified the phenotypic plasticity of the periwinkle Littorina brevicula across a natural estuarine gradient by applying untargeted LC-MS/MS metabolomics and a combination of traditional and 3D morphometric approaches. Individuals were collected at the Liuqinghe River estuary at two salinity regimes: high salinity in the low intertidal and low salinity in the high intertidal. Traditional morphometric analysis revealed significantly larger aperture height and aperture shape index in the high intertidal group, while overall shell proportions and three-dimensional surface descriptors did not differ significantly between stations, suggesting that aperture shape is the morphological trait most responsive to the estuarine gradient. A combined univariate and multivariate approach identified 765 differentially expressed metabolites and 11 significantly enriched pathways, indicating broad reprogramming of core biosynthetic networks. Methylamines, hypotaurine and taurine accumulated in the low intertidal group, consistent with osmoregulatory adjustment to high-salinity conditions. Malic acid and fumaric acid, biomarkers of anaerobic metabolism in invertebrates, are significantly upregulated in the high intertidal group. The high intertidal snails presented higher concentrations of polyunsaturated fatty acids, consistent with membrane remodelling under chronic environmental stress. Metabolic plasticity exceeded morphological divergence across the estuarine gradient, suggesting that physiological responses may provide the primary mechanism enabling persistence under highly variable intertidal conditions. These results highlight the metabolome's plasticity under the pressure of multiple environmental stressors, forcing periwinkles to prioritise short-term homeostasis over energetically costly functions. By linking salinity-driven metabolic reprogramming to potential shifts in individual performance, these findings suggest that physiological plasticity in intertidal ectotherms may scale up to affect population persistence, consumer-resource interactions and the resilience of estuarine communities under intensifying environmental variability.