Agriculture is one of the most important resources of polluting water. Water pollution that is created from agriculture activities is mostly due to the use of Chemical fertilizer, pesticides and herbicides. Nitrate and Phosphate are two significant pollutants which are created from chemical fertilizer, and cause surroundings pollution including water resources. There are different techniques for cleaning environment from polluted metals that most of these techniques are very costly, time-consuming and destructive for environment. Among these Buffer zones with phytoremediation process is a natural method of cleaning the pollution caused by agriculture system. This method is very effective, low cost and has scientific benefits and its performance ability is feasible for long time. In this research a experiment was carried out in order to study the phytoremediation ability of Ailanthus altissima Mill and Fraxinus excelsior. L in Buffer zones. To achieve the goals 96 trees of the two species were planted in the properties of Isfahan University of Technology. Nitrate and phosphate pollutants were investigated in four densities of 0-5-10-50 (mg/L). Afterward the remove level of nitrate and phosphate pollutants and also some physiologic plants factors such as chlorophyll and conductivity were measured. The results show that nitrate removal in 5, 10 and 50 mg/L concentration in the frist week by A . altissima are 74.53%, 75.23%, 79.95% and by F . excelsior are 79.04%, 80.65%, 83.97% respectively. Also, phosphate removal in 5, 10 and 50 mg/L by A . altissima are 74.16%, 77.18%, 82.81% and by F . excelsior are 74.16%, 79.87%, 83.56% respectively. Therefore, even though the quantity of nitrate and phosphate removal by F . excelsior is more than A . altissima . Yet, the removal potential of the two species are almost similar and the differences are not significant for phosphate in whole concentrations and the same for nitrate in 5 and 10 mg/L. Consequently, F . excelsior has ahigher nitrate removal potential in 50 mg/L concentration. Adding nitrate and phosphate up to 10 mg/L concentration more activity of plant and increment in both stomatal conductivity (25.33 mmol/m2.s ) and chlorophyll(15.76 spad value) than to control. Higher concentration of 50 mg/L results in sever decrease in both conductivity (4 mmol/m 2 .s) and amount of chlorophyll (2.05 spad value) than to control in plant. that means physiologic disorders. Keywords: Pollution, riparian buffer zone, phytoremediation, woody species, Agricultural contaminants.