Two humic acids (HAs) were isolated from contaminated river sediments present under comparative conditions in the Pearl River Basin, China. YFHA (the HA extracted at an open pyrite mining area in Yunfu) exhibited a lower absorption intensity for certain bands in the Fourier transform infrared spectra, a lower E4/E6 value (the UV absorbances at 465 nm (E4) and 665 nm (E6)), a lower apparent molecular weight, a lower polarity and a lower oxygen functionality in comparison with GZHA (the HA isolated at an urban living area in Guangzhou). All these differences indicated a higher degree of humification of YFHA than GZHA. Overall, the enrichment patterns of permanent heavy metals in the studied HAs were similar to those in corresponding sediments. In particular, YFHA exhibited high enrichment of trace element T1, a characteristic concomitant from the mining of the pyrite minerals. The adsorption isotherms of two HAs for goethite and pyrolusite, two representative geological materials, conformed to the Langmuir equation. Based on the qualitative relationships between the Langmuir constants of the adsorption isotherms and the chemical characteristics of HAs, the main mechanism of HA adsorption on these materials was suggested to be hydrophobic interaction. This study highlighted the promising use of HA as a peculiar bio-indicator of uncommon trace metal contaminations. The HA adsorption mechanism on representative geological materials further provided a theoretical basis for the study on the unusual metal behavior in complex environmental settings.