During the past six decades, agriculture as a main sector in Iran’s economy has been affected by economic development, land-use policies, and population growth and its pressures. From the 1940s until 2010, the percentage of the total urban population of Iran increased from about 21 % to around 72 %. Urbanization, industrialization, and intensive cultivation have dramatically affected soil and water resources. The exploitation of groundwater has been increased around fourfold from the 1970s to the mid-2000s. Total water resources per capita reduced around 23 % from 1956 to 2008. The average annual decrease in the groundwater table in Iran during the last two decades is 0.51 m. In 2008, the groundwater table fell around −1.14 m in average in Iran. The average use of chemical fertilizers increased from around 2.1 million tons in 1990s to about 3.7 million tons in 2009. During that period, fertilizer use efficiency decreased from around 28 % to around 21 %. Approximately 77 % of the agricultural land under irrigation suffers from different levels of salinity. According to the quantification of four indices, such as soil erosion, fall in groundwater levels, salinity, and use of chemical fertilizer, that are directly related to agricultural land use, the results show that agricultural management in Iran needs special attention to reach sustainable conditions. The total cost of soil and water degradation and use of fertilizers in agriculture are estimated around than US $12.8 billion (about 157,000 billion IRRials)—approximately 4 % of the total gross domestic product (GDP) and approximately 35 % of the GDP of the agricultural sector in Iran.