Climate change disproportionately affects the Arctic, where warming is up to four times greater than the global annual average experienced in southern regions. Baffin Bay in the Canadian Arctic Archipelago is an ecologically and biologically significant area that will likely experience an increase in marine vessel traffic as a result of consistent declines in annual sea ice coverage. Along the western coast of Baffin Bay is known to be a region of active, natural hydrocarbon seeps where elevated levels of methane have been detected in previous surveys. Petroleum hydrocarbons released from the seafloor can fuel microbial production and shape the baseline microbiome. Establishing a microbial baseline is highly valuable as it contributes to a fundamental understanding of the existing microbial diversity that may be impacted in the future by anthropogenic stressors. In this study, 16S and 18S rRNA gene amplicon sequencing surveys revealed that the vertical stratification of the water column is largely driven by differences in depth, temperature, salinity, and inorganic nutrient concentrations. Chemical analysis provides further support that active petrogenic methane seepage occurs around Cape Dyer but not in areas targeted in this study. Presence of n-alkanes and toluene in association with hydrocarbon-synthesizing phytoplankton suggests biogenic production of these compounds. These findings provide a baseline for future environmental monitoring assessments to evaluate how the prokaryotic and eukaryotic microbiome may be impacted by ongoing climate change and anthropogenic stressors in western Baffin Bay.