The lead‑zinc smelter at Trail (British Columbia, Canada) has operated continuously for ∼125 years, with long-standing concerns that transboundary metal(loid) and sulphur emissions have contaminated water bodies in both western Canada and Washington (WA), USA. To assess aquatic ecosystems affected by over a century of industrial contamination requires an understanding of pre-smelting conditions. Here, we use a dated sediment core from Williams Lake (WA), downwind of both the Trail and the short-lived LeRoi (Northport, WA) smelters, to track regional contaminant history and other environmental stressors. Specifically, we examine a selection of chemical elements, cladoceran assemblages, visible range spectroscopy-inferred chlorophyll a (VRS-Chl a) and visible near-infrared spectroscopy-inferred lake-water total organic carbon (VNIRS-TOC). Sedimentary proxies recorded the onset of smelting in 1896 CE, peak periods of aerial emissions in the early to mid-20th century, and the history of emission controls. With a few exceptions, sedimentary metal(loid)s exceeded Canadian Interim Sediment Quality Guidelines during the height of the smelting era and have declined substantially since ca. 2000 CE. The loss of metal-sensitive Cladocera and declines in primary production (VRS-Chl a) at the onset of the regional smelting era indicate a strong biological response to airborne industrial contamination. The largest cladoceran change in the sediment record was concurrent with accelerated mitigation efforts at the Trail facilities following the 1960s; however, this compositional shift was between ecologically similar daphniid taxa. Steep declines in VNIRS-TOC concentrations during the period of peak emissions at Trail suggested an increase in sulphur deposition on the landscape that reduced terrestrial carbon supply. However, the persistence of calcium-sensitive daphniids throughout the record indicates that alkaline Williams Lake had not acidified. Current cladoceran assemblages remain substantially distinct from pre-industrial communities, demonstrating how paleoecotoxicological approaches can be used to track the effects of multiple stressors in a temporally appropriate context.