The dataset details organic carbon content of sediments across 6 intertidal sites in the winter and summer of 2013. The data provide a quantitative measure of the organic carbon present within surface sediments (up to a depth of 2 cm). Three sites were located in Essex, South East England and the other 3 in Morecambe Bay, North West England. Each site consisted of a saltmarsh habitat and adjacent mudflat habitat. 22 sampling quadrats were placed in each habitat covering 4 spatial scales. 3 replicate samples of surface sediment were collected at each quadrat. They were then processed for organic carbon content using the Loss on Ignition method (detailed below) Values are expressed as a percentage of the total sample collected. This data was collected as part of Coastal Biodiversity and Ecosystem Service Sustainability (CBESS): NE/J015644/1. The project was funded with support from the Biodiversity and Ecosystem Service Sustainability (BESS) programme. BESS is a six-year programme (2011-2017) funded by the UK Natural Environment Research Council (NERC) and the Biotechnology and Biological Sciences Research Council (BBSRC) as part of the UK's Living with Environmental Change (LWEC) programme. Full details about this dataset can be found at https://doi.org/10.5285/d4e9f0f7-637a-4aa4-b9df-2a4ca5bfaded