Industrial mercury (Hg) sources associated with the processing of Athabasca oil sands (AOS), Alberta, Canada, may pose an environmental risk to nearby water bodies via either waterborne or airborne transport. Using a dataset derived from 63 lakes in the area, this study investigates the relationships between total-Hg (THg), organic matter, grain size, and lake ecology as measured by environmentally sensitive arcellacean (testate lobose amoebae) communities. The lakes studied include 59 lakes within a 75 km radius of the operations, plus four distal lakes ~150 km from the main industrial operations. Hg transport to the lakes is primarily through airborne pathways. The four distal lakes in the Peace–Athabasca Delta (~150 km downstream of the AOS operations) were examined to determine if the operation is emitting potential waterborne inputs, in addition to airborne inputs, and to identify any associated impact to those ecosystems. Total mercury in lakes close to the AOS were similar to values recorded in lakes farthest away. THg was most closely linked to the silt fraction, suggesting much of the Hg in these lakes is minerogenic in origin, either adsorbed and/or lattice-bound. THg is not statistically related to organic matter as has been observed in other Canadian lakes. The ecologic response to THg levels was investigated via the distribution of key indicator species and, or species diversity (Shannon diversity index). The spatial extent of arcellacean ecosystem stress in the study lakes did not correlate with THg concentrations. This is perhaps due to the generally low THg levels found in these lakes, all except one had THg concentrations lower than current CCME guidelines. While these findings may rule out any direct link between THg concentrations in the lakes and observed Arcellacea faunas, ecosystem stress unrelated to THg was observed northeast of the AOS, which warrants further examination. The results of this research suggest that the natural lake arcellacean faunas in the region are not being significantly impacted by current THg concentrations.