The dataset details macrofaunal biomass across 6 intertidal sites in the winter and summer of 2013. The data provide a quantitative measure of the biomass of individual invertebrate species present within the top 10cm of sediment. 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 cores of sediment were collected at each quadrat. They were sieved on a 0.5mm mesh and the macrofauna was removed, identified to species (or appropriate taxon) and individuals of each species weighed. Values for macrofaunal biomass are expressed as grams per square metre of sediment. Biomass data for mudflat habitats across Essex and Morecambe are complete, however, saltmarsh data is only available for one full Essex site (Tillingham Marsh), in one season (winter) and across all sites, at the 1m scale. 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.