Northern terrestrial ecosystems are undergoing rapid transformation, potentially affecting the chemistry and microbial community structure in rivers flowing through them. The Sheldrake River flows through permafrost degradation and vegetation gradients resulting from the influence of Hudson Bay on the coastal climate. From 23 to 27 August 2019, we sampled surface waters along a hydrological continuum flowing through this permafrost and vegetation gradients, as well as a salinity gradient. This sampling includes Sheldrake Lake and River, the Sheldrake River plume flowing into Hudson Bay, the coastal waters of Hudson Bay, and an unnamed tributary of the Sheldrake River. This limnological and pigment dataset is complementary to an amplicon dataset (prokaryotes and microbial eukaryotes) available at the NCBI Sequence Read Archive (BioProject: PRJNA803180). It includes data for nutrients (total nitrogen and phosphorus), carbon (dissolved organic and inorganic), dissolved organic carbon characterization (SUVA254, SR, a320, S289), cell abundance measured by flow cytometry, salinity, temperature, oxygen, major cations, pH, specific conductivity, total suspended sediment concentration, and pigments determined by high-performance liquid chromatography.
