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Lakes of the Bécancour River Basin (BRB), located in the former asbestos mining region of Thetford Mines (southern Quebec, Canada), are heavily exposed to pollution. A previous paleolimnological investigation revealed that Trout Lake underwent severe eutrophication following the drainage of former Black Lake for mining purposes in the 1950s. Questions remained regarding the causes and level of degradation of other BRB lakes located upstream (Lake Bécancour) and further downstream (lakes William and Joseph), which also suffer from eutrophication. This paper presents diatom analyses performed on sediment cores from these lakes, along with complementary carbon (C) and nitrogen (N) data, that fill this knowledge gap. It also provides new insights into the natural limnological history of the Thetford Mines region. Low planktonic to benthic diatom ratios in oldest Lake Bécancour sediments revealed lower water levels during the Holocene Thermal Maximum (ca. 9000–5500 cal years BP). They later increased while diatom-inferred water pH decreased in response to cooler and wetter climatic conditions. Lake William responded more strongly than other BRB lakes to anthropogenic settlement activities in its watershed, with the emergence of Aulacoseira subarctica marking its transition to a mesotrophic state at about 1885 CE. Similar to Trout Lake, the drainage of Black Lake further enhanced the eutrophication of lakes William and Joseph, as illustrated by increases in sediment δ13C, decreases in C/N ratios, and proliferation of nutrient-dependent species such as Cyclostephanos invisitatus/makarovae. Our study highlights long-lasting and dramatic effects of such hydrological interventions on multi-lake systems. [ABSTRACT FROM AUTHOR]