Soil salinity due to irrigation is a major constraint to agriculture, particularly in arid and semi-arid zones, due to water scarcity and high evaporation rates. Reducing salinity is a fundamental objective for protecting the soil and supporting agricultural production. The present study aimed to empirically measure and simulate with a model, the reduction in soil salinity in a Vertisol by the cultivation and irrigation of Echinochloa stagnina. Laboratory soil column experiments were conducted to test three treatments: (i) ponded bare soil without crops, (ii) ponded soil cultivated with E. stagnina in two successive cropping seasons and (iii) ponded soil permanently cultivated with E. stagnina with a staggered harvest. After 11 months of E. stagnina growth, the electrical conductivity of soil saturated paste (ECe) decreased by 79-88% in the topsoil layer (0-8 cm) in both soils cultivated with E. stagnina and in bare soil. In contrast, in the deepest soil layer (18-25 cm), the ECe decreased more in soil cultivated with E. stagnina (41-83%) than in bare soil (32-58%). Salt stocks, which were initially similar in the columns, decreased more in soil cultivated with E. stagnina (65-87%) than in bare soil (34-45%). The simulation model Hydrus-1D was used to predict the general trends in soil salinity and compare them to measurements. Both the measurements and model predictions highlighted the contrast between the two cropping seasons: soil salinity decreased slowly during the first cropping season and rapidly during the second cropping season following the intercropping season. Our results also suggested that planting E. stagnina was a promising option for controlling the salinity of saline-sodic Vertisols.