Facility agriculture enhances food production capabilities. However, concerns persist regarding heavy metal accumulation resulting from extensive operation of this type of farming. This study integrated the total content, five fractions, and isotope composition of Cd and Pb in intensively farmed soils in regions characterized by industrialization (Shaoguan, SG) and urbanization (Guangzhou, GZ), to assess the sources and mechanisms causing metals accumulation. We found significantly more severe Cd/Pb accumulation and potential mobility in SG than GZ. Cd displayed higher accumulation levels and potential mobility than Pb. The distinct isotopic signals in SG (−0.54 to 0.47‰ for δ^114/110Cd and 1.1755 to 1.1867 for ²⁰⁶Pb/²⁰⁷Pb) and GZ (−0.86 to 0.12‰ for δ^114/110Cd and 1.1914 to 1.2012 for ²⁰⁶Pb/²⁰⁷Pb) indicated significant differences in Cd/Pb sources. The Bayesian model revealed that industrial activities and related transportation accounted for over 40% and approximately 30%, respectively, of the average contributions of Cd/Pb in SG. While urban-related (26.6%) and agricultural-related (26.3%) activities primarily contributed to Cd in GZ. The integration of δ^114/110Cd and ²⁰⁸Pb/²⁰⁶Pb has further enhanced the regional contrast in sources. The present study established a comprehensive tracing system for Cd-Pb, providing crucial insights into the accumulation and distribution of these metals in facility agricultural soils.