Soil salinization is a critical global issue for sustainable agriculture, impacting crop yields and posing a threat to achieving the Sustainable Development Goal (SDG) of ensuring food security. It is necessary to monitor it in detail and uncover its underlying factors at a regional scale. In this context, the present study aimed to evaluate soil health in the eastern Mediterranean region by using the Sodium Adsorption Ratio (SAR) as an indicator of soil salinity in three distinct soil horizons. The main objective of the research was to evaluate the performance of four machine learning (ML) models, including Random Forest (RF), Nu Support Vector Regression (NuSVR), Artificial Neural Network-Multi Layer Perceptron (ANN-MLP), and Gradient Boosting Regression (GBR), for accurate prediction of SAR following the Recursive Feature Elimination (RFE) as a feature selection method. Moreover, SHapely Additive exPlanations (SHAP) was applied as sensitivity analysis to identify the most influential covariates. Main findings of the research revealed that the average clay content in the surface horizon (H10-25cm) was 50.5% ± 10.4, which significantly increased to 57.5% ± 8.7 (p < 0.05). No significant mean differences were detected between the studied horizons for SAR and Na+. ML output revealed that NuSVR outperformed other algorithms in accurately predicting outcomes during both the training and testing stages. Moreover, Scenario 2 (SC2) with seven selected features from the RFE method facilitated highly accurate SAR predictions. Overall, the performance of ML models is ranked as NuSVR > GBR > ANN-MLP > RF. Lastly, SHAP sensitivity analysis identified CEC, Ca+2, Mg+2, and Na+ as the most influential variables for SAR prediction in both the training and testing stages. Hence, the research yielded valuable insights for efficient agricultural soil management at a regional level using state-of-the-art technology.