A field-based study was carried out by researchers and students from the Geography Department, University of Victoria to improve upon existing knowledge of water cycling, biogeochemical processes and acid sensitivity of lakes in complex, ungauged areas of the Boreal Forest in the Oil Sands region NE Alberta. Sponsored by the Cumulative Environmental Management Association and the Natural Sciences and Engineering Research Council of Canada, the research involved detailed studies at two lake/watershed sites near Fort McMurray (NE07 and SM08) during 2005 to 2009, supported by regional water surveys of 48 additional lakes/watersheds monitored during 2000-2009 as part of the Regional Aquatics Monitoring Program. The research program utilized an array of physical, geochemical, and isotopic techniques aimed at providing information required to assess present and future trends in critical acid loadings to aquatic ecosystems in areas broadly affected by NOxSOx emissions from the bitumen refining operations. Overall the study has confirmed that site-specific estimates of water yield (a.k.a. runoff) are necessary when applying critical loads models to lakes in the region. This study has also tested and identified a number of practical local- and regional-scale approaches for characterization of water yield to lakes, critical loads of acidity, and for determining relative importance of various pathways of water flow to lakes. These are important variables required to predict acidification using dynamic models such as the Model for Acidification of Groundwater In Catchments (MAGIC). Together with wetland classification mapping by CEMA collaborators, this study also has provided a broader understanding of hydrologic organization of watersheds in wetland-dominated areas, and has uncovered the existence of a systematic relationship between land cover types, permafrost distribution, and water yield to lakes. These findings contribute to a sharper focus on potential impacts of acid deposition from oil sands operations and establish and test new tools for site-specific, regional-scale critical loads assessment in complex wetland-dominated terrain.