Several limnological and paleolimnological investigations have linked enhanced atmospheric nitrogen (N) deposition to nutrient enrichment and increased primary production. The Athabasca Oil Sands Region (AOSR) in northeast Alberta, Canada is a significant source of N emissions, particularly since development intensified during the 1990s, and recent paleolimnological investigations provide evidence of increased lake production in adjacent areas subject to enhanced N deposition. The AOSR, however, has also experienced atmospheric warming since ca. AD 1900, and therefore the relative effects of nutrient deposition and climate changes on lake production remain unclear. We undertook a factorial-design paleolimnological assessment of 16 lakes in northwest Saskatchewan to quantify changes in abundance and species composition of scaled chrysophytes over the past 100 years. Study sites included both N-limited and P-limited lakes within control regions, as well as lakes that receive enhanced N deposition from the AOSR. We hypothesized that a change in algal communities within N-limited AOSR-impacted lakes, without concurrent changes in the other lake groups, would suggest AOSR-derived N as a driver of enhanced primary production. Instead, marked increases in concentrations of scaled chrysophytes, mainly Mallomonas crassisquama, occurred in the recent sediments in cores from all four lake groups (N-limited vs. P-limited, impacted vs. control), suggesting that regional climate change rather than N deposition was the paramount process enhancing chrysophyte production. Because chrysophyte abundances tended to be higher in deep, lower-pH lakes, and chrysophyte time series were fit best by lake-specific generalized additive models, we infer that climate effects may have been mediated by additional catchment and/or lake-specific processes.