The marine carbon cycle in Canadian Arctic waters, particularly in Nares Strait and Baffin Bay, is undergoing rapid change due to a shifting climate. Despite this, there's been a paucity of research into the carbonate chemistry and biogeochemical processes in these regions. This thesis addresses this gap by investigating the complex carbon dynamics in these waters, critical for understanding their role in the global carbon cycle. The first research chapter evaluates the strength of the biological carbon pump during the spring ice-edge bloom in Baffin Bay. We found stark differences in springtime net community production (NCP) between Arctic and Atlantic water domains, in western and eastern Baffin Bay, respectively. Arctic outflow waters exhibited low spring NCP (< 1 mol C m-2) due to persistent sea-ice cover and strong stratification of the upper water column, whereas the Atlantic water domain displayed high NCP rates (up to 5.7 mol C m-2). The first comprehensive examination of the marine carbon dynamics in Nares Strait is also presented. Using a multi-tracer linear mixing model, we distinguished the role of physical and biological processes on the distribution of dissolved inorganic carbon in Nares Strait. We identified water mass mixing as the dominant control on marine carbon dynamics, with primary production also playing an important role in decreasing surface pCO2. Importantly, this investigation also provided the first documented evidence of Siberian river waters arriving in Nares Strait. The final research chapter of this thesis investigates the biogeochemical processes affecting aragonite saturation states (ΩAr), and the state of ocean acidification in Baffin Bay, with a focus on the west Greenland continental shelf region, which has remained under-studied in terms of its marine biogeochemistry. We identify two main depth-dependent processes shaping the ΩAr distribution throughout Baffin Bay; within the upper 200 metres, lower ΩAr coincides with increasing fractions of Arctic-outflow waters, while below 200 metres organic matter respiration is responsible for decreasing ΩAr. Surprisingly, substantial Arctic-outflow waters were identified on the west Greenland shelf, challenging what is currently known of circulation patterns in the bay, and underscoring the need for further research.