The absence of well-executed environmental monitoring in the Athabasca oil sands (Alberta, Canada) has necessitated the use of indirect approaches to determine background conditions of freshwater ecosystems before development of one of the Earth’s largest energy deposits. Here, we use highly resolved lake sediment records to provide ecological context to ∼50 y of oil sands development and other environmental changes affecting lake ecosystems in the region. We show that polycyclic aromatic hydrocarbons (PAHs) within lake sediments, particularly C1-C4–alkylated PAHs, increased significantly after development of the bitumen resource began, followed by significant increases in dibenzothiophenes. Total PAH fluxes in the modern sediments of our six study lakes, including one site ∼90 km northwest of the major development area, are now ∼2.5–23 times greater than ∼1960 levels. PAH ratios indicate temporal shifts from primarily wood combustion to petrogenic sources that coincide with greater oil sands development. Canadian interim sediment quality guidelines for PAHs have been exceeded since the mid-1980s at the most impacted site. A paleoecological assessment of Daphnia shows that this sentinel zooplankter has not yet been negatively impacted by decades of high atmospheric PAH deposition. Rather, coincident with increases in PAHs, climate-induced shifts in aquatic primary production related to warmer and drier conditions are the primary environmental drivers producing marked daphniid shifts after ∼1960 to 1970. Because of the striking increase in PAHs, elevated primary production, and zooplankton changes, these oil sands lake ecosystems have entered new ecological states completely distinct from those of previous centuries.