<p>Lakes in high-latitude regions are recognized as sentinels for the detection and monitoring of impacted environments and climate change. Tursujuq Park is a &gt; 27,000 km² protected area in subarctic northern Quebec (Canada) that is the site of numerous lakes that to date are poorly studied. We investigated 49 lakes spanning across the park to understand the diversity of limnological conditions, establish the regional diatom flora, and determine diatom autecological preferences. We identified 462 diatom taxa from 50 genera and found significant differences in diatom community composition between coastal and inland sites, and within the inland area between lakes with catchments dominated by coniferous and shrub vegetation. The environmental variables pH, total nitrogen, total phosphorus and dissolved inorganic carbon were strongly related to diatom assemblage composition. This study makes important advances in understanding the limnology and ecology of a critical subarctic reference region and will enable future lake biomonitoring and management programs in Nunavik for the detection and remediation of the effects of environmental change.</p>