In arid and semi-arid regions, where water scarcity and soil salinization are major challenges, carob (Ceratonia siliqua L.) has gained attention as a potential drought- and salt-tolerant crop. However, its ability to withstand salt stress is determined by a complex interplay of genetic, physiological, and environmental factors, which requires a comprehensive approach to fully understand. This study aims to explore the resilience of carob to salt stress by integrating advanced multivariate methods, Partial Least Squares Structural Equation Modeling (PLS-SEM), and Artificial Intelligence-assisted Bayesian Inference to identify key determinants of stress tolerance. Through a Multivariate Analysis of Variance (MANOVA), we found significant effects of salt stress (F(5,30) = 7.3637, p < 2.2e-16) and ecotype (F(5,30) = 16.4968, p < 2.2e-16) on physiological and biochemical traits. The Principal Component Analysis (PCA) revealed a distinct separation between stressed and control plants, with the first principal component (PC1) explaining 76.66% of the variance, which was closely related to biomass, water content, and root length. The PLS-SEM model identified root length as the primary factor influencing biomass (coefficient = 0.629, p < 0.05), while water content and chlorophyll had no direct significant effect. Hierarchical Bayesian Inference allowed for the assessment of intra-population variability, showing that the Ouazzane provenance exhibited the highest salt resistance, followed by Safi and Aït Attab, while Khemissat proved the most vulnerable. Additionally, specific environmental effects (E[i]) demonstrated that certain provenances, such as Berkane and Aït Attab, benefitted significantly from co-cultivation with Spergularia salina under 10 g/L NaCl. These findings underline the importance of varietal selection and biotic interactions as effective strategies to mitigate salt stress, highlighting the potential for agroecological adaptation of carob to increasingly saline environments, offering valuable insights for sustainable agricultural practices in areas affected by salinity.