Background soils are frequently utilized as a surrogate to assess pollution levels and environmental risks of heavy metals in Chinese lakes. However, there remains a lack of understanding regarding the reliability and uncertainty of such assessments. Here, we determined heavy metals (As, Cd, Co, Cr, Cu, Hg, Ni, Pb, and Zn) in sediment cores from five rural lakes in North China to evaluate the reliability and uncertainty of the assessments using background soils by comparing them with assessments based on background sediments. Comparative studies reveal large uncertainties in the assessments using background soils. Among these metals, uncertainties for Hg and Cd are relatively large, whereas those for the other metals are minor. This discrepancy is due to the considerably higher natural variability of Hg and Cd in soils and sediments in comparison to the other metals. Generally, assessments utilizing background soils underestimate pollution levels and risks of Hg but overestimate those of Cd in these lakes. Despite limited human activities around the lakes, they still received a considerable influx of heavy metals via regional atmospheric transport. Assessments of the nine metals indicate moderate to considerable ecological risks in these lakes. The risks are contributed primarily (78–89%) by Hg and Cd. This study underscores the substantial uncertainties in assessing heavy metal pollution and risks using regional background soils and emphasizes the importance of controlling atmospheric emissions of Hg and Cd to mitigate pollution in rural and remote water bodies in China.

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