The contamination of surface and ground waters by nitrogen and phosphorus is a major factor affecting estuarine eutrophication and drinking water supplies in many countries. Considering agriculture, Non-point source (NPS) pollution from croplands has reduced water quality in rivers and lakes around the world. So this study was aimed to introduce buffer zones as an effective way that reduces water pollution and also investigating their structure and function in nitrogen and phosphorus removal as an agricultural pollutant. Unfortunately, studies on buffer zones are very limited in our country. Due to the importance of Zayandehrud as a main river of the country on which the life of Isfahan city is dependent, Zayandehrud and agricultural land around this river were selected as the study area. At first, Zayandehrud margins were identified by Google earth software for the buffer zones associated with agricultural land which mostly consisted of paddy fields and had nitrogen and phosphorus pollutions. Then, structure and function of buffer zones were investigated through field studies. Measurement of perimeter, area, length, latitude and longitude and typology of Buffer zone spots are important structural characterizes that play a key role on buffer zones function and they have been studied in this research. After that, samples were taken in parallel transects at the beginning, middle and at the end of the field at the depth of 30 cm and then nitrogen and phosphorus pollution was determined in laboratory. Results have shown that buffer zone is such an effective approach in nitrogen and phosphorus removal that their amounts reduced from the beginning of field to the end of the buffer zone.