The database compiles published data (in Serrano et al. 2016, Biogeosciences, doi:10.5194/bg-2015-598) on biogeochemical characteristics (%organic carbon, stable carbon isotopes and mud content) of sediments underneath seagrass meadows and bare sediments in Australia and Spain. Details on habitat characteristics (latitude/longitude, water depth, seagrass species and geomorphology) and sediment depth are also provided for each location studied. The data set includes 1345 data entries from 100 sediment cores, encompassing 10 seagrass species in estuarine and coastal habitats. Enquiries about the dataset may be sent to Oscar Serrano firstname.lastname@example.org.