The objective of this study was to investigate the long-term cultivation effects on soil properties changes in different geomorphic surfaces of an arid region in eastern Iran. Surface soil samples (0–30 cm) were collected at 160 locations from five geomorphic surfaces under pomegranate (Punica granatum L.), pistachio (Pistacia vera L.), and saffron (Crocus sativus L.) cultivations in 2004 and 2018. The results showed that dune field geomorphic surface (i.e., CK111) had significantly higher electrical conductivity (EC), soluble cations, including Caaq, Mgaq, Naaq, and sodium adsorption ratio (SAR) due to the high salinity of the irrigation water. The highest and lowest soil organic carbon (SOC), available phosphorus (Pav), and available potassium (Kav) values were in the soils under clay flats (i.e., PL111) and CK111, respectively, which positively correlated with clay content. Total nitrogen (TN) was higher in geomorphic surfaces, including pediment with recent and old alluvial deposits (Pi311 and Pi321) and CK111, which were under extensive pistachio orchards. On the other hand, due to the intensive agricultural practices and soil management, the amount of Pav decreased except in Pi321 through 14 years, while Kav has increased in most units. Overall, the results of this study revealed that during long-term cultivation, the size of the areas with high (12 to 16 dS m− 1) and very high (16 to 32 dS m− 1) salinity and alkalinity classes were increased in the studied regions, especially in pistachio cultivation during irrigation with inadequate water in playa margin lands. Moreover, increasing air temperature and rainfall reduction through recent years, water shortage and salinity, and over-extraction of groundwater are significant factors in increasing the concentration of EC and SAR of water and soil. Consequently, the planning for agricultural development in the region should be done considering the problems and limitations of unsustainable agricultural development on the edge of the desert.

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