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The Athabasca Oil Sands Region (AOSR) in northeast Alberta contains Canada’s largest reserve of hydrocarbons, and the third largest in the world. Extraction and processing operations generate contaminants and nutrients that are aerially deposited across the region. However, structured environmental monitoring efforts were only initiated decades following the establishment (1967) and escalation (~ 1980) of commercial operations. We examined whether diatom assemblages preserved in 210Pb-dated sediment cores retrieved from strategically selected lakes have responded to aerial deposition of contaminants. The relative amount of contaminant inputs was tracked using sedimentary dibenzothiophene (DBT) concentrations and DBT enrichment factors, which are established proxies for AOSR activities. We observed no relationship between diatom assemblage changes and DBT enrichment. The nature of the diatom changes differed among lakes, regardless of DBT enrichment, suggesting that diatom responses were related to site-specific conditions. Moreover, diatom assemblage changes at several sites tracked trends in whole-lake primary production. Collectively, these records indicate that regional warming is likely the primary driver of recent diatom assemblage changes in these shallow, closed-basin lakes.