The growth of world population and the demand for agricultural products can be regarded as one of the important issues that humanity has ever faced. There are serious concerns regarding surface and ground water pollution by nitrates because of using nitrogen fertilizers in the agriculture. Improving agricultural water management systems can reduce nitrate in drainage outflow and therefore, reduce the environmental pollution. This research was conducted to evaluate the effect of the controlled drainage and nitrogen fertilizer on nitrate leaching and environment pollution as a factorial randomized complete block design in Shiraz College of Agriculture. The treatments consisted of three fertilizer levels; 0, 200 and 300 kgN/ha, and three water table depths: free drainage, control water table at 60cm (CD60) and 90 cm (CD90) depths, respectively. According to the results, the value of drainage water and nitrate losses in the controlled drainage toward free drainage were significantly increased. The mean reduction of drainage water in CD60 and CD90, as compared to free drainage, was 59.3 and 35.7%, respectively. The decrease nitrate losses, as compared to free drainage, was 72 and 44%, respectively. The total value of nitrate leaching in 200 and 300 kgN/ha fertilizer treatments was 1.86 and 2.48 times of 0 kgN/ ha.