<p>Potentially toxic elements (PTEs) in agricultural soils of geological high-background areas often reflect parent material composition, influencing their uptake by crops. However, the pathways and sources of PTEs in cropping systems derived from diverse geologies remain unclear. This study investigated soil-rice systems in typical high-background areas underlain by phosphorite, black shale, and basalt. We analyzed PTE contents in paddy soils and rice grains to determine their transfer and enrichment patterns. Lead isotopes and Positive Matrix Factorization (PMF) were employed to quantify PTE sources. Results showed that soils from phosphorite were significantly enriched in Pb, As, and Hg, resulting in mild composite enrichment of rice grains by Cd, Pb, As, Hg, and Cr. Black shale-derived soils exhibited marked Cd and Zn enrichment, leading to notable Cd contamination in grains. Basalt-derived soils were enriched with Cr, Ni, and Cu, with rice grains accumulating significant levels of Cr and Ni. Source apportionment revealed that PTEs originated from geological background, agricultural activities, traffic emissions, and coal combustion. Notably, PTEs from the phosphorite geology accumulated in topsoil but showed lower bioavailability than those released from weathered black shale and basalt. Specifically, Cd and Cu from black shale, and Zn, Ni, and Hg from basalt, demonstrated high bioavailability. This study identifies dominant PTEs and their accumulation pathways in diverse geological systems, providing a scientific basis for ensuring rice safety and managing PTE risks in agricultural systems with diverse geological backgrounds.</p>