Fjords provide an important ecological service by burying and storing organic carbon (OC) more rapidly than most other marine environments. Quantifying this OC sink regionally requires an understanding of both the burial and remineralization processes that determine net OC sequestered. Within two sites from two Nunatsiavut fjords (Nachvak Fjord and Saglek Fjord, Labrador, Canada), we measured geochemistry associated with carbon, oxygen, and nutrient cycling and used a 1-D reactive transport model with an inverse modelling approach to simulate the geochemistry in the sampled sediment. A lower OC burial rate in sediment from Nachvak Fjord likely reflected significantly lower OC content in surface sediments and bottom sediments. Nachvak Fjord sediment modelling yielded a higher nitrification rate and a higher nitrate-dependent iron oxidation rate despite low heterotrophic denitrification compared to Saglek Fjord model results. Findings from microbial 16S rRNA gene sequencing were consistent with modelled biogeochemistry results from both fjords considering relative contributions from nitrate and sulfate reduction. Significantly higher OC content in Saglek Fjord sediments aligned with ~2X OC burial annually compared to Nachvak Fjord sediments. Differences in OC content and biogeochemical cycling might result from relative location chosen for sampling within each fjord, noting that we sampled outer fjord sediments in Nachvak Fjord, and inner fjord sediments in Saglek Fjord. Nevertheless, despite cold temperatures and good ventilation, both fjord basins utilized denitrification pathways (heterotrophic or nitrate-dependent iron oxidation) as the dominant nitrogen sink. Using both OC burial rates as end members, we estimate that northern Nunatsiavut fjords collectively store 8,000–33,000 tonnes OC yr^−1. Our findings underscore the importance of additional studies with process-based measurements paired with OC burial estimates to understand further how climate change may alter benthic cycling and OC storage.