Soil salinity and sodicity are the major environmental issues that lead to the deterioration of soil properties, nutrient cycling, and soil ecosystems around the globe. Nevertheless, the reciprocal effects of salinity and sodicity levels on depth-wise soil organic matter (SOM) and micronutrients remain elusive, particularly in Thailand. For a better understanding of such an issue, soil samples were collected from 38 sites at depths of 0–20, 30–50, 60–80, and 80–120 cm where they were affected by salts with variable levels of salinity and sodicity, having electrical conductivity (ECe), and exchangeable sodium percentage (ESP) from 0.20–74.70 dS m–1, and 2.74%–113.23%, respectively. Soil physicochemical properties, including distribution of sand, silt, and clay, pH, soil organic carbon (SOC), and micronutrients (Fe, Zn, Mn, Cu, and B) were determined. The results exhibited that SOC content, ranging from 3.36–14.74 g kg–1, was higher in topsoil (0–20 cm) compared to the other three soil depths and it correlated negatively with ECe (0–20 and 80–120 cm) and ESP (80–120 cm), suggesting the declines in SOC amount due to high salinity and sodicity levels. Topsoil Mn concentration (0.06–182.06 mg kg–1) also tended to be greater than the other soil depths while Fe concentration in that soil depth (0.02–33.99 mg kg–1) tended to be smaller. The ECe correlated negatively with the concentrations of Fe, Cu (all soil depths), and Zn (30–50 and 60–80 cm), and positively with Mn concentration (60–80 and 80–120 cm), suggesting that the availability of Fe Cu and Zn is vulnerable to high salinity and sodicity levels. Overall, our findings highlight that high salinity and sodicity levels brought about a reduction in SOC content and low concentrations of micronutrients in soils, irrespective of Mn concentration.