In this study, the quality of groundwater aquifer of Gavkhooni basin was investigated in agriculture. For this purpose, water quality data related to 96 wells prepared by Isfahan Regional Water Authority during the statistical period 2015-2016 were used. In this study, sodium parameters, electrical conductivity, chloride, hydrogen bicarbonate and sodium absorption ratio (SAR) were used. Then, groundwater quality classification across the study area was carried out using agricultural water quality index (IWQI), which is based on the  FAO standards. Results of IWQI varied  from  40 to 80, corresponding to high and low limitations for agricultural use. It was shown that groundwater quality had  declined over years from the upstream to the downstream of the basin. Furthermore, some changes in the quality index in the northern region of the study area were found to be more affected by the climate conditions of the region. In the middle and eastern territories, the surface streamflow of Zayandehroud River and agricultural activities had  caused changes in the  water quality. In general, in the Gavkhooni area, excessive groundwater exploitation, drought conditions and agricultural activities had reduced the groundwater quality. By reducing groundwater withdrawals and agricultural activities in areas where water is required only through water drainage, groundwater quality can be managed, even in dry years.