The SOx and NOx emissions created by the oil sands industry in Alberta have the potential to cause acidification, eutrophication and increase trace metal accumulation in freshwaters in the area. Relationships between benthic macroinvertebrates (BMI) and water chemistry were calculated and a bioassessment was conducted to determine whether there was a difference in BMI assemblages between test and reference lakes. A Reference Condition Approach (RCA) was used to determine whether BMI in test lakes were different from reference lakes because an appropriate historical dataset was unavailable. Test lakes were located in an area where modeled S deposition was elevated, while reference lakes were selected in areas of "minimal disturbance" and maximized chemical and physical similarities with test lakes through an Assesssment by Nearest Neighbours Analysis (ANNA)-type grouping technique. Three analyses were used to robustly compare BMI composition at test and reference lakes, One Sample T- Tests, Multivariate Analysis of Variance (MANOVA) and a Test Site Analysis (TSA). A pilot study was also carried out to determine the mercury (Hg) concentrations in Amphipoda and Chironomidae and to distinguish whether Hg concentrations were influenced by distance to Hg emissions in the Athabasca Oil Sands Region (AOSR). A Redundancy Analysis (RDA) showed that BMI communities were strongly affected by pH and DOC. Hyalellidae and Gammaridae were found in lakes with high pH values while Chironomidae and Oligochaete were found in lakes with low pH values. Dysticidae, Leptophlebidae, Corixidae, Sphaeriidae and Leptoceridae were more common in lakes with low DOC concentrations. Significant differences between BMI assemblages at test and reference lakes were identified by the One Sample T-Tests and MANOVA, while TSA identified potential differences in composition at 3 of the 5 test lakes according to a more lenient and reportedly, more ecologically meaningful approach. The differences in substrate and vegetation between test and reference lakes was likely more important in the causation of these differences than atmospheric deposition. Mercury concentrations in BMI were relatively high; accumulation was related to lake pH but not distance to a major Hg emission source. Chemically, the test lakes do not presently appear impacted from atmospheric pollution and because of the study design and the variable environment the differences in BMI cannot be attributed to SO* and NO* emissions. Nonetheless, appropriate field methods, analytical techniques and a dataset were developed so that future bioassessments can evaluate the effects of the growing oil sands industry more effectively than was previously possible.