Climate change is evidently altering the biogeochemical behavior of heavy metals (HMs) and persistent organic pollutants (POPs) in agrarian soils, intensifying their mobility, bioavailability, and environmental risk. This study synthesizes over two decades of global literature to evaluate how rising temperatures, erratic precipitation, and extreme weather events modify the fate and transport of key contaminants such as cadmium (Cd), lead (Pb), polychlorinated biphenyls (PCBs), and dioxins in agricultural ecosystems. A 10°C increase in soil temperature can elevate Cd desorption by 30%, while typhoon-induced sediment remobilization increases polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofuran (PCDD/F) fluxes in tropical reservoirs from baseline levels of 2.4–20 ng I-TEQ/m2/year. Climate-driven hydrological shifts enhance contaminant leaching, as observed in subtropical monsoonal regions where Cu and Zn runoff increase by 3.1% and 2.2%, respectively, during high-rainfall events. POPs show increased volatilization and long-range transport under warming scenarios, with model simulations indicating a 10% rise in hexachlorobenzene (HCB) and dichlorodiphenyl dichloroethylene (DDE) volatilization per 1°C increase in air temperature. Soil degradation, microbial destabilization, and reduced organic matter content under climate stress compound these effects, facilitating pollutant bioaccumulation in crops and trophic transfer. Regional disparities in pollutant burden are evident, with Asia and sub-Saharan Africa experiencing high legacy and emerging contamination due to industrialization, agrochemical use, and limited regulatory enforcement. While frameworks such as the Stockholm and Minamata Conventions have reduced atmospheric concentrations of targeted POPs and Hg by over 80% in regulated regions, enforcement gaps persist globally. Urgent actions for adaptive, climate-resilient soil management and dynamic risk-based regulation are advocated.