Salinity is one of the most common water quality threats in river basins and irrigated regions worldwide. Available watershed models, however, do not simulate the fate and transport of salt species. This paper presents a modified version of the popular SWAT watershed model that simulates the transport of major salt ions in a watershed system. Salt is transported via surface runoff, soil percolation, groundwater flow, and streamflow. The model can be used in salt-affected watersheds worldwide.