Groundwater is the most important source of fresh water needed for agriculture, drinking water, and industry. Industrial development population growth and increasing demand of human consumptions have imposed damage to the nature. Industrial development with extra utilization, regardless of their potential, has led to irregular use of water resources and contaminating these resources, so that only a limited range of natural resources is currently left available. Unfortunately, many of these changes and abandonments have been caused by anthropogenic impacts and use. In this regard, water resources and natural ecosystems as the ultimate recipient of pollution have suffered the most damages from development. Assessing the quality of groundwater through continuous monitoring is the basis for planning to control and reduce ground water pollution. In this regard, water quality index (WQI) which can be expressed in a single scale can play a very important role for determining the quality of groundwater quality.In this research, in order to calculate the qualitative indices (IRWQI GC , IWQI, WHOWQI) in Govkhini Basin, monthly physical and chemical parameters, water level of piezometric wells and hydrometric stations during 21 years period (1995-2016), 15 units of Govkhooni basin in the province of Isfahan Located in the Isfahan Regional Water Authority were selected. Also, in order to study the effective factors of agricultural water quality changes, the agricultural statistics of crop production were obtained from the Agricultural-Jihad Organization of Isfahan Province and rainfall data were obtained from Isfaha meteorological stations. In addition, the trend analysis of groundwater quality indicators and its chemical parameters will be analyzed using the Man-Kendall test. The IRWQI GC , WHOWQI indicator, states that about 75% of the groundwater quality status is in poor and bad conditions for drinking and public consumption. For IWQI, about 68% of the groundwater basin has moderate agricultural constraints. In general, spatial variations and, in addition, the trend of the three indicators show that the water quality has declined from the upstream to downstream over time. According to the results obtained, in the northern regions of the climatic conditions are the most important factor affecting the quality of groundwater quality, while to the downstream reaches of the basin, the quantity of agriculturalproduction, the level of groundwater level and surface water flow are effective factors on the groundwater quality. It seems that if the necessary measures to control the exploitation of groundwater resources and the use of chemicals fertil;it use in agriculture and other effective measures in this basin are not carefully taken, there will be a graduate decline in the quality of groundwater in more areas of the basin, resulting in problems for drinking water and agriculture water supply and may put the economic and social situation at risk. In general, the use of qualitative indicators (IRWQI GC , IWQI, WHOWQI) as a criterion for determining the pollution level and groundwater quality in a standard framework, as well as for assessing the improvement of aquifer condition are suggested in the future. Keywords : Groundwater Quality, Groundwater Quality Indices (IRWQI GC , IWQI, WHOWQI), Man-Kandal Test, Trend Analysis, Gavkhoni Basin.