Lithology-Stratified Geochemical Baselines Reveal Reference-Scale Effects on the Classification of Potentially Toxic Elements in Agricultural Soils

Uniform geochemical baselines can obscure natural variation among geological units, whereas local baselines may become unstable when sample sizes are limited. This study analyzed 209 agricultural topsoil samples from a geologically heterogeneous county for Cd, Hg, As, Pb, Cr, Cu, Ni, and Zn. Five baseline methods were compared, and county-wide, lithology-stratified, and soil-type-stratified reference frameworks were evaluated using breakpoint support, bootstrap stability, between-group differentiation, and classification changes. Cumulative probability analysis identified supported breakpoints for all eight elements, with ΔBIC values of 72.8–455.9 and valid bootstrap proportions of at least 99.2%. Lithology stratification showed stronger between-group differentiation than soil-type stratification and provided coverage by local baselines meeting the application criteria of 91.4% for seven elements and 71.3% for Cr. Local upper reference breakpoints differed from county-wide values by −80.4% to 191.2%, reclassifying 16.3–34.4% of samples. After adjustment for lithological group means, multi-element local deviations remained spatially autocorrelated, with Moran’s I = 0.112 and p = 0.003. Lithology-specific references identified samples whose classification depended on reference scale. They can support targeted investigation and differentiated management but should be used alongside risk-based regulatory thresholds.