Seagrass ecosystems provide an array of ecosystem services ranging from habitat provision to erosion control. From a climate change and eutrophication mitigation perspective, the ecosystem services include burial and storage of carbon and nutrients in the sediments. Eelgrass (Zostera marina) is the most abundant seagrass species along the Danish coasts, and while its function as a carbon and nutrient sink has been documented in some areas, the spatial variability of these functions, and the drivers behind them, are not well understood. Here we present the first nationwide study on eelgrass sediment stock of carbon (Cstock), nitrogen (Nstock), and phosphorus (Pstock). Stocks were measured in the top 10 cm of eelgrass meadows spanning semi-enclosed estuaries (inner and outer fjords) to open coasts. Further, we assessed environmental factors (level of exposure, sediment properties, level of eutrophication) from each area to evaluate their relative importance as drivers of the spatial pattern in the respective stocks. We found large spatial variability in sediment stocks, representing 155-4413 g C m-2, 24-448 g N m-2, and 7-34 g P m-2. Cstock and Nstock were significantly higher in inner fjords compared to outer fjords and open coasts. Cstock, Nstock, and Pstock showed a significantly positive relationship with the silt-clay content in the sediments. Moreover, Cstock was also significantly higher in more eutrophied areas with high concentrations of nutrients and chlorophyll a (chl a) in the water column. Conversely, silt-clay content was not related to nutrients or chl a, suggesting a spatial dependence of the importance of these factors in driving stock sizes and implying that local differences in sediment properties and eutrophication level should be included when evaluating the storage capacity of carbon, nitrogen, and phosphorus in Danish eelgrass meadows. These insights provide guidance to managers in selecting priority areas for carbon and nutrient storage for climate- and eutrophication mitigation initiatives.