By removing nutrients from the water, coastal ecosystems serve as a filter between land and the open sea. Seagrasses contribute to the coastal filter by trapping and absorbing nutrients. Understanding the processes and environmental conditions underpinning the variability in nutrient retention among and within seagrass meadows is important to evaluate their role in the coastal filter across geographic regions, especially in less studied regions. This study evaluates the role of eelgrass (Zostera marina) meadows in the coastal filter in boreal Newfoundland, Canada, and identifies environmental traits driving variability in nutrient fluxes. We measured carbon (Corg) and nitrogen (N) proportions and stable isotopic composition in the surface sediment (top 5 cm) of three eelgrass meadows. Sediment cores were collected from different locations (i.e., inside, edge, outside) relative to each meadow. Sediment %N (0.22%), %Corg (2.82%), Corg stock (11.1 Mg Corg ha−1), and N stock (0.91 Mg N ha−1) were elevated in our study sites; however, nutrient content was not consistently higher inside the meadow than at the edge or outside. Variability in nutrient retention was best explained by a negative relationship with sediment bulk density. Additionally, differences in carbon isotopic (δ13Corg) enrichment between eelgrass tissue (−11.6‰) and sediment (−22.1‰) within sites indicated that sediment nutrients were predominantly derived from allochthonous marine sources, where variability was best explained by salinity. This study improves the understanding of the role of eelgrass to nutrient cycles in boreal coastal systems and the potential of eelgrass as a blue carbon ecosystem.