Phosphorus is one of the main pollutants of agricultural surface drainage; that over standard doze of it cause eutrophication in surface water resource. This study investigates evaluation the ability of Semnan's zeolite, that modified by hexadecyltrimethylammonium, to removal phosphorus under flow conditions in agricultural drainage. In this regard, after modifying natural zeolite, at first was absorption kinetics, adsorption isotherms, affecting of pH and temperature experiments on phosphorus removal conducted by modified zeolite in laboratory scale. The experiments were done in 3-5 mm size of zeolite for investigating effect of zeolite size on phosphorus removal. In order to assess the flow conditions on phosphorus removal physical model of agricultural drainage and the modified zeolite filter ponds were constructed in length of 2, 3 and 5 cm. The both discharge 0.05 and 0.1 lit/s were applied in drainage and changes of phosphorus concentrations were measured at various times after passing through the filter ponds. The sorption kinetic experiments showed maximum phosphorus removal by modified zeolite occurred in the first 2 hours. Moreover, percent phosphorus removal with increasing the pH from 3 to 8 decreased and increased from 8 to 12. Also percent removal with increasing temperature in the range of 17 to 30 °C decreased. The results showed Langmuir isotherm had good agreement for explan phosphorus removal by modified zeolite. The results of physical model showed that higher percent phosphorus removal occurred in higher discharge and lower length of filter pond due to more contact drain water with the modified zeolite.