Development of the Athabasca Oil Sands Region (AOSR) in northern Alberta, Canada has resulted in the substantial release of emissions, such as reactive nitrogen (Nr) species and base cations, which can fertilize downwind lakes in the boreal forest of Saskatchewan. However, to address the potential impacts of nutrient deposition on these algal communities, interpretations must occur in the context of ongoing regional climate change. Here, I use a factorial paleolimnological analysis to isolate the unique effects of AOSR emissions and climate change on lake geochemistry (C and N stable isotopes and elemental content) and algal assemblages (fossil pigments) over the past ~100 years. Surveyed lakes were either nitrogen (N)- or phosphorus (P)-limited and were located either within an impacted area receiving enhanced AOSR-derived deposition or within an unaffected reference region. Common trends from generalized additive models indicated that all algal groups declined after 1980 in P-limited lakes receiving deposition, coinciding with industrial intensification of the AOSR. In contrast, total algal abundance (as β-carotene and declining C/N ratios) as well as abundances of mixotrophic cryptophytes (alloxanthin) and unicellular cyanobacteria (echinenone, but not canthaxanthin) increased regionally in reference and impacted, N-limited lakes since the mid-1900s. Biomarkers from obligate autotrophs, and sedimentary δ13C and δ15N values, changed asynchronously among lakes, reiterating a fundamental restructuring of the algal community. These patterns suggest that regional climate change has intensified primary production in Saskatchewan boreal lakes and increased cyanobacteria and mixotrophic phytoplankton abundance. However, oligotrophication of impacted, P-limited sites suggests a change in nutrient export from the catchment. Specifically, increased terrestrial vegetation growth due to enhanced nutrient deposition likely resulted in subsequent diminishing of P export to these lakes. This study provides the first evidence of detrimental effects of industrial development on remote downwind lakes. Moreover, I outline a potential mechanism that incorporates a holistic view of how unique effects of the AOSR and climate change have influenced algal community composition over the last century in boreal SK. Careful evaluation of the current and future AOSR industrial footprint is required to fully understand the ramifications of development on Canada’s economy and environment.