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[Display omitted] • Recent soils by land reclamation had a fingerprint of sediment in PTE distribution. • Intense and long-term diffuse sources elevated PTE level in old alluvial soils. • Agriculture-derived As and Cd led to bias in GBV calculated from the whole area. • GBV were established on subarea based on PTE source contribution. • Source-based GBV avoid underestimation of PTE contamination from diffuse sources. Intense input of potential toxic elements (PTEs) from diffuse anthropogenic sources to agricultural alluvial soils has caused bias in the geochemical baseline value (GBV) established by current methods. This study intends to assess the extent of bias and establish the GBV for 9 PTEs based on their source contribution on the largest alluvial islands in China, the Chongming Islands. The results of total PTE concentrations in soil samples (n = 120) showed that the islands were influenced by PTEs from various diffuse sources. Source identification methods provided a common conclusion that Ni, Co and Cr were dominated by the Yangtze River sediment input and thus more enriched in "recent" alluvial soils which were generated by large-scale reclamation practices. Positive matrix factorization quantified that pesticides and mineral fertilizer contributed 84.3% of As and 63.6% of Cd, especially in "old" soils, while a large proportion of Cu, Sb, Pb and Zn came from atmospheric deposition. Accumulation of PTEs was enhanced by soil sorption phases including organic matter and clay. Because of this differentiation in source contribution, the GBV of As, Cd, Co and Ni established on "recent" soils are significantly different from those established on data from the whole area. Using this source-based GBVs, the geoaccumulation index method suggested that 37% and 25% of the sampling sites were contaminated by As and Cd, respectively. This study emphasized the importance of considering different sources contribution in GBV determination to avoid underestimation of enrichment of PTEs from intense human diffuse sources. [ABSTRACT FROM AUTHOR]