This study explores the applicability of Artificial Neural Networks (ANNs) for predicting salt build‐up in the crop root zone. ANN models were developed with salinity data from field lysimeters subirrigated with brackish water. Different ANN architectures were explored by varying the number of processing elements (PEs) (from 1 to 30) for replicate data from a 0.4 m water table, 0.8 m water table, and both 0.4 and 0.8 m water table lysimeters. Different ANN models were developed by using individual replicate treatment values as well as the mean value for each treatment. For replicate data, the models with twenty, seven, and six PEs were found to be the best for the water tables at 0.4 m, 0.8 m and both water tables combined, respectively. The correlation coefficients between observed salinity and ANN predicted salinity of the test data with these models were 0.89, 0.91, and 0.89, respectively. The performance of the ANNs developed using mean salinity values of the replicates was found to be similar to those with replicate data. Not only was there agreement between observed and ANN predicted salinity values, the results clearly indicated the potential use of ANN models for predicting salt build‐up in soil profile at a specific site.