Understanding the carbon sequestration potential of blue carbon ecosystems is important to inform climate policies and to guide restoration and protection efforts. Alkalinity generation is an often overlooked carbon sequestration mechanism, especially in seagrass meadows. Here, we quantified total alkalinity (TA) and dissolved inorganic carbon (DIC) fluxes in two cold-temperate Zostera marina seagrass meadows in Sweden using 24-h in-situ chamber incubations at the end of the high-productivity season. The seagrass meadows were similar net sources of TA (16 ± 45 mmol m⁻² d⁻¹ in Smalsund, 17 ± 16 mmol m⁻² d⁻¹ in Bökevik), whereas DIC fluxes were highly variable (34 ± 59 mmol m⁻² d⁻¹ in Smalsund, −43 ± 35 mmol m⁻² d⁻¹ in Bökevik). Fluxes followed a diurnal cycle consistent with photosynthesis-respiration cycles. As a result, seagrass meadows ameliorated ocean acidification locally during the day, but not during the night. The large CO₂ uptake provided higher buffering levels compared to mangroves and saltmarshes. The TA fluxes were comparable to those reported for Mediterranean and tropical seagrass meadows, but 16-times lower than in mangrove forests and 5-times lower than in saltmarshes. Alkalinity generation in these cold-temperate seagrasses exceeded soil organic carbon stocks accumulation by fourfold, potentially contributing to their carbon sequestration potential and warranting inclusion in seagrass meadow carbon budgets.