A human activities can affect river water quality are fish farming development projects. In this study, with design and construction of natural filters in the fish farms, the output water quality changes will be investigated. For this purpose, a series of columns (PVC tubes) with height of 70 cm was used to investigate changes in nitrate and phosphate. Any tube divided in half and in the middle of it was placed a geotextile layer. Then the variety of materials such as beet pulp, wheat bran and maize to a height of 10 cm was poured into pipes and water continuously for 4 hours from the column was passed. Then the inlet and outlet were taken samples at different times. The results showed nitrate absorbing in wheat bran and maize have become increasing-decreasing trends and sugar beet pulp absorption over time, as is decreasing. Also, the percentage of phosphate absorption in sugar beet has an increasing trend and in maize and wheat bran have increasing-decreasing trends in the duration of 4 hours. So, among the three agricultural materials, maximum of nitrate and phosphate absorptions in wheat bran is taken and Nitrate absorption is more than three other materials. Also, the results show significant differences between treatments in one percent probability level in terms of nitrate and phosphate output. On the other hand, with a significant interaction between treatments output over different periods can be understood that the plant material selected as the filters have a high potential to absorb nitrates and phosphates.