Boating activities are one of the causes that threaten seagrass meadows and the ecosystem services they provide. Mechanical destruction of seagrass habitats may also trigger the erosion of sedimentary organic carbon (Corg) stocks, which may contribute to increasing atmospheric CO2. This study presents the first estimates of loss of Corg stocks in seagrass meadows due to mooring activities in Rottnest Island, Western Australia. Sediment cores were sampled from seagrass meadows and from bare but previously vegetated sediments underneath moorings. The Corg stores have been compromised by the mooring deployment from 1930s onwards, which involved both the erosion of existing sedimentary Corg stores and the lack of further accumulation of Corg. On average, undisturbed meadows had accumulated ~6.4 Kg Corg m−2 in the upper 50 cm-thick deposits at a rate of 34 g Corg m−2 yr−1. The comparison of Corg stores between meadows and mooring scars allows us to estimate a loss of 4.8 kg Corg m−2 in the 50 cm-thick deposits accumulated over ca. 200 yr as a result of mooring deployments. These results provide key data for the implementation of Corg storage credit offset policies to avoid the conversion of seagrass ecosystems and contribute to their preservation.