Agroforesty systems, which are recommended as a management option to lower the shallow groundwater level and to reuse saline subsurface drainage waters from the tile-drained croplands in the drainage-impacted areas of Jan Joaquin Valley of California, have resulted in excessive boron buildup in the soil root zone. To assess the efficacy of the long-term impacts of soil boron buildup in agroforesty systems, a mathematical model was developed to simulate non-conservative boron transport. The developed dynamic two-dimensional finite element model simulates water flow and boron transport in saturated-unsaturated soil system, including boron sorption and boron uptake by root-water extraction processes. The simulation of two different observed field data sets by the developed model is satisfactory, with mean absolute error of 1.5 mg/L and relative error of 6.5%. Application of the model to three different soils shows that boron adsorption is higher in silt loam soil than that in sandy loam and clay loam soils. This result agrees with the laboratory experimental observations. The results of the sensitivity analysis indicate that boron uptake by root-water extraction process influences the boron concentration distribution along the root zone. Also, absorption coefficient and maximum adsorptive capacity of a soil for boron are found to be sensitive parameters.