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Obtaining groundwater of a suitable quality for irrigating crops can be difficult in semi-arid regions in low-income countries like Iran, particularly under conditions where annual rainfall may be declining due to the effects of climate change. Due to substantial difference in the melon production of two important groundwater basins in the Jim-Abad and Torbate-Jam areas in northeastern Iran, groundwater was sampled from 23 wells from these basins and chemically analyzed for physicochemical parameters appropriate for irrigation. These data were used to determine sodium adsorption ratio (SAR), salinity hazard (SH) and irrigation water quality index (IWQI) values and were subjected to statistical assessment to determine the key factors that influence the chemical composition of groundwater in the area. The results of the IWQI survey indicated that 67% of groundwater samples from the Jim-Abad plain and all but one of the samples from the Torbate-Jam plain had a severe limitation for irrigation use. A Piper plot indicated that groundwater quality in the two basins was dominated by sodium and chloride ions. A Gibbs plot suggests that evaporation is the dominant control on groundwater quality in the two basins, although there appears to a significant influence of water-rock reactions in the Torbate-Jam basin. An assessment of the data using cluster analysis and principal component analysis suggests that carbonate dissolution under the influence of the common ion effect also has a significant effect on the quality of groundwater in the region.