In this paper, we compare the elemental and isotopic (C, N, Pb) geochemistry of lake sediments from two contrasted environments in south‐central Chile. The first lake, Laguna Chica de San Pedro (LCSP), is situated in the urbanised area of the Biobio Region (36°S). The second lake, Lago Puyehue (40° S), is located 400 km to the southeast of LCSP and within an Andean national park. Our aim is to identify environmental impacts associated with increasing industrial activities and land degradation during the last 150 a. In LCSP, shifts in C/N atomic ratios, δ13C and δ15N from 1915–1937 to the late 1980s are attributed to successive land degradation episodes in the lake watershed. Based on a Pb isotopic mixing model, we estimate that up to 20% of lead in LCSP sediments is supplied from urban atmospheric pollution. By contrast, human impact in the watershed of Lago Puyehue is very limited. We observe no change in organic geochemistry during the last 150 a and lead contamination remains lower than 5%, even during the last decades. Although contamination levels are much higher in LCSP than in Lago Puyehue, a peak in anthropogenic Pb is recorded during the same period (1974–1976) at both sites. This maximum contamination level is consistent with increased industrial activity in the vicinity of Concepción. Copyright © 2010 John Wiley & Sons, Ltd.