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Substances found in watersheds and sediments in artisanal and small-scale gold mining (ASGM) areas contaminated by heavy metals are becoming tremendously critical issues in Asia. This study aimed at clarifying the pollution caused by heavy metals in sediments in river basins near ASGM sites in Gorontalo Province, North Sulawesi, Indonesia. Sediment samples collected from experimental areas were classified into nine clay samples and twenty-seven sand samples, whereas three other samples were collected from the control area. Particle-induced X-ray emission was used to analyze these samples. The Statistical Package for the Social Science and the geo-accumulation index (Igeo) were also used for analysis. Based on the results, Hg, Pb, As, and Zn had a concentration of 0–334 µg/g, 5.5–1930 µg/g, 0–18,900 µg/g, and 0–4923.2 µg/g, respectively, which exceeded limits recommended by the U.S. Environmental Protection Agency consensus (1991) and the Indonesian Government Regulation Number 38, 2011. Furthermore, Igeo showed the order of the pollution degree Hg < Zn < Pb < As and reflected an environment contaminated by heavy metals, ranging from unpolluted to extremely polluted areas. Therefore, sediments contaminated by Hg, Pb, As, and Zn could be found along the river basin of mining areas.