Despite studies focusing on soil substrates (carbon and nitrogen) and heavy metal availability, the impact of diversified parent materials in arid alkaline regions has received little attention. To reveal the influence of parent material, we investigated four different parent materials: fluvio-marine, Nile alluvial, lacustrine, and aeolian deposits. We assessed the effect of soil parent materials through selected soil physical and chemical properties, such as clay content, bulk density, pH, and available phosphorus (AP). The Tukey HSD test (SPSS ver. 23) was used to assess the soils derived from these different sediments. Using the R “glmulti” package, we examined this effect in a model of mixed-effects meta-regression. The sum of Akaike weights for models that contained each element was used to estimate the importance of each factor. The average contents of soil organic carbon (SOC) and total N in alluvial deposits were greater (p < 0.001) than those of marine, aeolian, and lacustrine deposits. A multivariate analysis in arid regions revealed that parent material, soil pH, and the availability of P had the greatest effects on SOC concentration, whereas clay content, available P, soil pH, parent material, and bulk density had the greatest effects on soil total nitrogen. The average content of Fe in the aeolian deposits was greater (p < 0.001) than those of marine, alluvial, and lacustrine deposits, without any significant differences between the latter two deposits. We found that the highest average contents of zinc (Zn), manganese (Mn), and copper (Cu) were recorded in alluvial deposits, with significant differences between other deposits. Soil parent material was the major factor impacting soil iron (Fe) content, along with clay content and soil pH. However, soil bulk density was the most important factor controlling soil Zn and Mn contents, while SOC drove Cu content. This study will help in developing a more accurate model of the dynamics of soil substrates and availability of heavy metals by considering readily available variables, such as parent materials, soil pH, soil bulk density, and clay content.