The dataset details larger mobile fish and macrofaunal abundance across six intertidal sites in the winter and summer of 2013, sampled using fyke nets. The data provide a quantitative measure of larger mobile invertebrate and fish species present in fyke nets caught over two executive tidal cycles at three sites in Essex, South East England and three more sites in Morecambe Bay, North West England. At each site, 22 sampling quadrats were placed on the mud flat covering 4 spatial scales. At each of these, unbaited fyke nets were deployed perpendicular to the shore over two tidal cycles. Upon removal, the species were identified to species level and individuals counted. For each species wet weight (g) was calculated. 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/10.5285/778ac3e5-a796-46a0-8390-0b6527598d8b