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The Republic of Azerbaijan suffers from low agricultural productivity caused by soil salinization and erosion, and limited and insufficient soil data are available for economic and political reasons. In this study, soil salinity and heavy metal levels were assessed. Environmental risk assessment was conducted to evaluate the potential risk posed by soils to human health. Soil guideline values were proposed to monitor soil pollution in the Republic of Azerbaijan. Water extraction and spatial variability analysis were conducted to understand soil salinization and heavy metal pollution. Among the 20 studied elements, the elements Ca, Cl, and S and the heavy metals Cr, Ni, and Pb were classified as problematic on the basis of the geoaccumulation index, and As was also identified as posing a possible risk on the basis of the potential ecological risk index. Based on the developed soil guideline values for agricultural soil, the As, Cr, and Ni in the soil samples exceeded their respective guidelines by 31.3, 41.8, and 61.6%, respectively. Water extraction results confirmed that 99% of the leached ions were cationic salts, and the most problematic ion was Na, followed by Ca, Cl, and S. The extractability values of Cr and Ni were significantly lower than those of other heavy metals, which implies that their actual leaching potential may be overestimated. The linear regression and spatial variability analysis confirmed that leachable salts have accumulated in lowland areas due to the capillary rise of water and evaporation, but the distribution of heavy metals confirmed that As, Cr, and Ni were abundant in agricultural soils. Our results clearly showed that heavy metal soil contamination and high salinity levels are major problems that should be considered when assessing food safety and health hazards in the Mugan Plain of Azerbaijan. Therefore, future studies should be performed for additional environmental risk assessment, detailed hazard identification, and health risk assessment.