Soil salinization and heavy metal pollution in the Yellow River Delta region have elicited increasing concern. Therefore, revealing the underlying mechanism of the impact of soil salinity on potential toxic elements (PTEs) is crucial for environmental protection and the rational utilization of resources in this area. In this study, we employed CatBoost–SHAP and multiscale geographically weighted regression (MGWR) models to comprehensively investigate the spatial effects of soil electrical conductivity (EC1:5) on PTEs. Additionally, we employed a space–for–time substitution strategy with the aim of investigating how increasing soil salinity, represented by EC1:5, K+, Na+, Ca2+, and Mg2+, affects the bioavailability of PTEs over time. The primary findings are as follows: (1) for most PTEs, the influence of soil EC1:5 on the bioavailable forms of these elements surpassed its impact on their total concentrations. (2) The results of the MGWR model indicated that exchangeable Ca (aCa) in the soils of the eastern coastal areas markedly increased the bioavailable Cd (aCd), bioavailable Cu (aCu), and bioavailable Zn (aZn). (3) When the soil EC1:5 ranges between 2 and 6 dS/m, exchangeable Na (aNa) primarily competed for the adsorption sites of bioavailable Pb (aPb). However, as the soil EC1:5 increases to 6–10 dS/m, exchangeable Mg (aMg) and aCa became the primary competing ions, with aMg playing a more significant role than aCa. These findings provide valuable theoretical insights and practical guidance for saline-alkali soil improvement and PTEs pollution control in the Yellow River Delta region, thereby providing a foundation for sustainable environmental management and resource utilization.