Cultivation of highly salt-tolerant plants (i.e., halophytes), may provide a viable alternative to increase productivity compared to conventional salt-sensitive crops, increasing the economic potential of salt-affected lands that comprise ~20% of irrigated lands worldwide. In this study the Agricultural Policy/Environmental eXtender (APEX) model was adapted to simulate growth of the halophyte quinoa, along with salt dynamics in the plant-soil-water system. Model modifications included salt uptake and salt stress functions formulated using greenhouse data. Data from a field site were used to further parameterize and calibrate the model. Initial simulation results were promising, but differences between simulated and observed soil salinity and plant salt values during the growing season in the calibration suggest that additional improvements to salt uptake and soil salinity algorithms are needed. To demonstrate utility of the modified APEX model, six scenarios were run to estimate quinoa biomass production and soil salinity with different irrigation managements and salinities. Simulated annual biomass was sensitive to soil moisture, and root zone salinity increased in all scenarios. Further experiments are needed to improve understanding of crop salt uptake dynamics and stress sensitivities so that future model updates and simulations better represent salt dynamics in plants and soils in agricultural settings.