Organic carbon (OC) storage in coastal vegetated ecosystems is increasingly being considered in carbon financing and climate change mitigation strategies. However, spatial heterogeneity in these “blue carbon” stocks among and within habitats has only recently been examined, despite its considerable implications. Seagrass meadows have potential to store significant amounts of carbon in their sediments, yet studies comparing sediment OC content at regional and meadow scales remain sparse. Here, we collected sediment cores from six temperate eelgrass (Zostera marina) meadows on the coast of British Columbia, Canada, to quantify sediment OC stocks, accumulation rates, and sources, and to examine local and regional drivers of variability. Sediment OC content was highly variable—across all sites, stocks in the top 0–5 cm ranged from 83 to 1089 g OC m−2, while the 15–20 cm stocks exhibited a 24‐fold difference, from 59 to 1407 g OC m−2. Carbon accumulation rates ranged from 4 to 33 g OC m−2 yr−1. Isotopic mixing models revealed that sediment OC was primarily terrestrial carbon (41.3%) and canopy‐forming kelps (33.3%), with a smaller contribution of eelgrass (25.3%). Here, we show that regional variability in OC content exceeds meadow‐scale variability. This result is likely driven by landscape factors, most notably relative water motion, representing a more dominant control on seagrass OC accumulation than meadow‐scale factors such as canopy complexity. These findings elicit caution when scaling up seagrass meadow OC content and demonstrate that measures of the hydrodynamic environment could improve estimates of carbon storage in temperate soft sediment habitats.