The anchoring of large recreational craft constitutes one of the main threats in shallow marine habitats. In the Mediterranean, this activity has seen constant development during the last decades, causing major physical disturbances in Posidonia oceanica meadows and associated ecosystem services. In this context, the main aims of the present study are to estimate the impact of this anchoring on P. oceanica meadows surface areas and carbon fixation and sequestration capacities, in a particularly highly-frequented area (Sant'Amanza bay, Corsica Island). Accurate benthic marine habitats mapping was performed yearly (2019–2021) using a drone coupled with ground-truthing data. The evaluation of carbon fixation and sequestration by the plant was measured at 12 stations within the bay (−5 m to −30 m). The maps of the marine habitats reveal an extensive regression of P. oceanica meadows (7.5 ha) between 2019 and 2020. This destruction represents a 9% decline in the total carbon fixation and sequestration performed each year by P. oceanica meadows within the bay. The related ecosystem services loss is estimated at 4.72 million € yr−1. Although an overall decline of boat anchoring in the seagrass meadow has been observed (e.g. recent enforcement of anchoring regulations), other solutions should be experimented to manage this major carbon sink.