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Abstract. Salinity is one of the most common water quality threats in riverbasins and irrigated regions worldwide. However, no available numericalmodels simulate all major processes affecting salt ion fate and transport at the watershed scale. This study presents a new salinity module for the SWAT model that simulates the fate and transport of eight major salt ions(SO42-, Ca2+, Mg2+, Na+, K+, Cl−,CO32-, HCO3-) in a watershed system. The module accountsfor salt transport in surface runoff, soil percolation, lateral flow,groundwater, and streams, and equilibrium chemistry reactions in soil layersand the aquifer. The module consists of several new subroutines that areimbedded within the SWAT modelling code and one input file containing soilsalinity and aquifer salinity data for the watershed. The model is appliedto a 732 km2 salinity-impaired irrigated region within the ArkansasRiver Valley in southeastern Colorado and tested against root zone soilsalinity, groundwater salt ion concentration, groundwater salt loadings tothe river network, and in-stream salt ion concentration. The model can be auseful tool in simulating baseline salinity transport and investigatingsalinity best management practices in watersheds of varying spatial scales.