Risk and susceptibility mapping of groundwater salinity (GWS) are challenging tasks for groundwater quality monitoring and management. Advancement of accurate prediction systems is essential for the identification of vulnerable areas in order to raise awareness about the potential salinity susceptibility and protect the groundwater and top-soil in due time. In this study, three machine learning models of Stochastic Gradient Boosting (StoGB), Rotation Forest (RotFor), and Bayesian Generalized Linear Model (Bayesglm) are developed for building prediction models and their performance evaluated in the delineation of salinity susceptibility maps. Both natural and human effective factors (16 features) were used as predictors for groundwater salinity modeling and were randomly divided into the training (80%) and testing (20%) datasets. The models were evaluated using testing datasets after calibration using the selected features by recursive feature elimination (RFE) method. The RFE indicated that modeling with 8 features had better performance among 1 to 16 features (Accuracy = 0.87). Results of the groundwater salinity prediction highlighted that StoGB had a good performance, whereas the RotFor and Bayesglm had an excellent performance based on the Kappa values (> 0.85). Although spatial prediction of the models was different, all of the models indicated that central parts of the region have a very high susceptibility which matches with agricultural areas, lithology map, the locations with low depth to groundwater, low slope, and elevation. Additionally, areas near to the Maharlu lake and locations with a high decline in groundwater are also located in the very high susceptibility zone, which can confirm the effects of saltwater intrusion. The susceptibility maps produced in this study are of utmost importance for water security and sustainable agriculture.