Bio-drainage can be considered as an important part of sustainable irrigation water management. Bio-drainage has potential for managing shallow water conditions in arid and semiarid areas especially when traditional subsurface drains are not available. Bio-drainage theory does not go back too far. The relationship between soil characteristics, water management regimes, and climatic conditions is not yet well defined. This study attempted to use a mathematical model (SAHYSMOD) to evaluate factors affecting design and operation of a bio-drainage system and study its sensitivity to different variables. The study showed that the major constraint of bio-drainage is salt accumulation in tree plantation strips in arid and semiarid regions. Maximum soil water salinity which can be controlled by bio-drainage is around 3 dS m−1 in rather medium run and sustainability may only be achieved where a salt removal mechanism is considered. The study also showed that the effectiveness of the system is higher where the neighboring strips are narrower. It also showed that bio-drainage is very sensitive to the amount of applied water. While the barrier depth does not have an important effect on water table draw down, it does have a great influence on lowering the salinization rate of tree plantation strips. The application of bio-drainage could be economically controversial since in humid areas water is sufficient for agricultural crops, allocating parts of the expensive land to mostly non-fruit trees may not be feasible, while in arid and semiarid regions there is usually enough cheap land to grow trees.