Northern terrestrial ecosystems are undergoing rapid transformation, potentially affecting the chemistry and microbial community structure in rivers flowing through them. From 2 to 10 August 2018, we sampled surface waters from the Great Whale River (GWR), three of its tributaries (Coats, Denys, and Kwakwatanikapistikw rivers), the GWR plume flowing into Hudson Bay, and the Sasapimakwananistikw River. This limnological and pigment dataset is complementary to an amplicon dataset (prokaryotes and microbial eukaryotes) available at the NCBI Sequence Read Archive (BioProject: PRJNA744875). It includes data for nutrients (total nitrogen and phosphorus, total dissolved nitrogen), carbon (dissolved organic and inorganic), dissolved organic carbon characterization (SUVA254, SR, a320, S289), cell abundance measured by flow cytometry, salinity, total suspended sediment concentration, and pigments determined by high-performance liquid chromatography.
