These data describe counts of macrobenthic infauna (with associated station metadata) taken from sediment samples collected at sites in the Tyne, Thames and Shoreham, UK from 2000 to 2006. For selected samples, wet biomass data is also included per taxon. The samples from the Shoreham site were collected across an aggregate extraction area over 4 years with the aim to test several habitat mapping techniques by documenting the presence of different faunal levels across the area. The samples collected at the Tyne and Thames were initiated at former sewage sludge disposal sites. Cefas conducted annual sampling in these areas during and post cessation of sewage disposal after January 1999 to monitor the benthic macrofauna community.