Seagrass meadows have a high ability to capture and store atmospheric CO₂ in the plant biomass and underlying sediment and thereby function as efficient carbon sinks. The seagrass Zostera marina is a common species in the temperate Northern Hemisphere, a region with strong seasonal variations in climate.

How seasonality affects carbon storage capacity in seagrass meadows is largely unknown, and therefore, in this study, we aimed to assess variations in sedimentary total organic carbon (TOC) content over a 1‐year cycle in seagrass meadows on the Swedish west coast. The TOC was measured in two Z. marina sites, one wave exposed and one sheltered, and at two depths (1.5 and 4 m) within each site, every second month from August 2015 to June 2016.

We found a strong seasonal variation in carbon density, with a peak in early summer (June), and that the TOC was negatively correlated to the net community production of the meadows, presumably related to organic matter degradation. There was seasonal variation in TOC content at all sediment sections, indicating that the carbon content down to 30 cm is unstable on a seasonal scale and therefore likely not a long‐term carbon sink.

The yearly mean carbon stocks were substantially higher in the sheltered meadow (3,965 and 3,465 g m⁻²) compared to the exposed one (2,712 and 1,054 g m⁻²) with similar seasonal variation. Due to the large intra‐annual variability in TOC content, seasonal variation should be considered in carbon stock assessments and management for cold‐temperate seagrass meadows.