Coastal eutrophication is one of the principal factors causing the loss of seagrass meadows worldwide. The loss of seagrass canopy after a disturbance may enhance the loss of sedimentary Organic Carbon (Corg) and Nitrogen (N) stocks through resuspension and remineralization, contributing to increased greenhouse gas emissions. This study presents comprehensive estimates of changes to Corg and N stocks and accumulation rates in seagrass meadows due to anthropogenic activities (e.g. eutrophication) and determines how habitat characteristics (e.g. bottom shear stress, water depth) influence the degree of nutrient fluxes at Cockburn Sound, WA. A total of 17 soil cores were sampled: 7 cores from living and persistent seagrass meadows, and 10 cores from bare sediments previously vegetated with seagrass. Sediment grain size was analysed to characterize sedimentary conditions and δ13C of sedimentary organic matter was used to determine the sources of Corg stocks at vegetated and un-vegetated sites. Accumulation rates of Corg and N were determined by means of 210Pb. On average, seagrass soils contained up to 2.5-fold higher Corg and N stores (3.32±0.5 and 0.16±0.15 kg m-2, respectively) than bare but previously vegetated sediments (1.45 and 0.11kg m-2) in 50 cm-thick deposits. Industrialization and land-use change in Cockburn Sound from 1960s onwards had led to the loss of 3,500 ha of seagrass ecosystems, linked to a loss of seagrass Corg and N sequestration capacity and the loss of sedimentary Corg (1.9 kg m-2) and N (0.05 kg m-2) stores accumulated over the last ~200 years. However, the loss of Corg and N stocks at Cockburn Sound was not homogenous. The areas with higher hydrodynamic energy experienced higher erosion and loss of stocks. This information is critical for the implementation of Corg storage credit offset policies centred on avoiding the conversion of seagrass ecosystems and contributing to their preservation, and to understand the role of seagrasses as filters and sinks of nutrients in a changing environment.