The purpose of this study was to predict and compare salt accumulation in the soil profile under drained and undrained conditions. The water management simulation model, Drainmod (Ver. 6.1) was used to determine the optimal drainage system design parameters, which will decrease soil profile salinity and provide maximum crop yields in Ankara-Bala Basin of Turkey. Soil sampling points were coordinated with the Global Positioning System (GPS). Soil, crop and site parameters were obtained as an input. The model was run for 5 years from 2005 to 2010 to simulate optimum drainage design parameters (drain depth, drain spacing) while controlling soil salinity in the root zone. Soil water conditions and soil salinity level were simulated for crop rotation of corn (Zea mays) and winter wheat (Triticum). Yield of individual crops was predicted for each growing season. The results of the simulations were analyzed to identify alternatives of subsurface drainage system that would satisfy maximum crop productions. According to the simulation results, the drain spacing of 130 m and drain depth at 160 cm are recommended for Bala Basin. Soil salinity maps were created for undrained and drained conditions. Results showed that the soil salinity level and salinity stress can be reduced and yield increased by installing a drainage system.