Abstract Background Seagrass and salt marsh ecosystems are recognised for their role in climate change mitigation and adaptation given their carbon storage potential. However, factors driving variability in blue carbon ecosystems are understudied, yet are important to account for. Aims Examine the variability of sediment organic carbon (SOC) and its drivers (seagrass morphometrics and sediment nutrients) at different spatial scales; > 1 km, ~ 150 m and ~ 10 m across the salt marsh-seagrass ecotone. Methods We collected the top 5 cm of sediment in the Olifants River Estuary, a cool-temperate system in South Africa. Using a line transect approach, we sampled across the salt marsh-seagrass ecotone (~ 10 m) in triplicate transects (~ 50 m apart) at three sampling sites (1–3 km) and analysed for SOC and elemental nutrient (nitrogen and phosphorus) content. Seagrass morphometrics (shoot density, leaf length and number per shoot) were measured. Results There was significant (P < 0.05) spatial heterogeneity in SOC stocks between sites (1–3 km) and between salt marshes and seagrass, but low variability at ~150 m. We detected a significant decrease in SOC from salt marsh towards the seagrass edge, with seagrass SOC remaining uniform. Nitrogen content was positively correlated with SOC in seagrass and salt marshes (P < 0.05), but seagrass morphometrics were not significant drivers of SOC. Conclusions The dynamics of blue carbon differ between salt marshes and seagrass, with spatial heterogeneity of SOC at scales > 1 km, suggesting that future BC assessments need to account for spatial heterogeneity to improve the accuracy of carbon removal estimates.