A major problem for irrigated agricultural production in arid and semi-arid environments is salinization of land. Irrigated land accounts for about one third of the world’s food, but nearly one fifth of irrigated lands are salt affected and suffer from reduced yield due to soil salinization. Most cultivated crops suffer from reduced yield when subjected to salt stress. However, about 1% of the world’s flora are known as halophytes, or plants that are capable of completing their life-cycle in higher saline soil or water environments. Halophytes are not commonly cultivated, but may be useful for human consumption, biofuel, or animal consumption. As a first step to assessing the potential of halophytic plants for salinity management, the Agricultural Policy/Environmental Extender (APEX) model was updated with a module to simulate plant-water-soil salinity dynamics using electrical conductance. The halophytes Atriplex nitens, Climacoptera lanata, and Salicornia europeae were parameterized in the APEX model’s plant database. Plant, soil, and water data from field sites in the Central Kyzylkum and Khorezm regions of Uzbekistan were used to set up APEX models for two field sites. Measured data collected from the two field sites in 2013 were used to assess model performance. Although APEX ran with the salinity module and produced output, analysis of the output indicated that further work is needed to produce a model that will be useful for assessing salinity management with halophytes. Suggestions for model improvements include enabling the modeling of individual salt ions because plants may experience toxic effects of different ions, and modeling detrimental effects of salt on conventional and halophytic plants. Additionally, future iterations of this project will benefit from more field data and experiments to measure plant parameters.