The Athabasca oil sands (AOS) represent one of Canada’s most economically important natural resources. Understanding the origin, fate and long-term impact of these industrial operations requires geoscientific knowledge of the potential environmental impacts. To quantify current impact an understanding of long-term environmental drivers is required. Here we utilize arcellaceans (testate lobose amoebae) to identify the peleoecologic history of the area, against which ecological stress associated with anthropogenic activities may be defined. Surface sediment samples were collected from 63 lakes forming a radius encompassing potential airborne and waterborne contaminate pathways. Total mercury (THg) in lakes close to the AOS were similar to values recorded in lakes farthest away and to values recorded in lakes surrounding coal fire plants in central Alberta. All lakes except one had THg concentrations lower than current CCME guidelines. The spatial extent of arcellacean ecosystem stress did not correlate with THg concentrations. To understand the long-term history of the AOS area a core (ALE) spanning 1,870 cal yr BP - present was used to assess how climate anomalies influence lake hydrology and ecology. Deconvolution of the grain size spectra indicates that populations are likely responding to overarching environmental controls. The coarser bedload material was interpreted to reflect high discharge events that occur during spring melts. A ratio of the coarse:fine fractions demonstrates abrupt oscillations of both high and low frequency and indicates that variation in spring melt volume and velocity was likely forced by climate change. Further investigation of the grain size data showed that the hydrologic character of ALE has responded to known ocean-atmosphere cycles, particularly the El Niño Southern Oscillation (ENSO) and that these cycles are underwent abrupt expression shifts every ca. 270-370 years. We attribute the expression shift to movement of the jet stream, which controls air mass distribution at this locality. An investigation of the ecological character of ALE from 1875 AD - present reveals that the arcellacean community was also influenced by climate anomalies and that decreased nutrient input, which is a function of precipitation during the El Niño phase of ENSO, applied stress to benthic ecology in these boreal lakes.