The presence-absence data for macrobenthic fauna that has been collected in Mingulay Reef Complex (Scotland, UK) across 79 stations over the years 2003, 2005, 2009, 2010 and 2011. The collection of the benthic samples has been carried out using a Van-Veen grab, mainly from hard habitats (e.g. live and dead coral framework). About 60% of the macrofaunal specimens have been identified at species level using high quality taxonomic keys and advice from taxonomy experts. Most common taxonomic groups analysed here are molluscs, polychaetes, arthropods, bryozoans, anthozoans, tunicates and brachiopods. The collection of the specimens is now deposited at the National Museums of Scotland (see the attached excel file for details). The enviromental data contains information about coordinates and environmental settings at stations where macrobenthic samples mentioned above, were collected. The environmental settings that are included in the file refer to the years 2003, 2005, 2009, 2010, 2011. For more information on the environmental variables have a look in Henry et al. 2010 (doi:10.1007/s00338-009-0577-6) and Henry et al. 2013 (doi:10.5194/bg-10-2737-2013). The environmental variables included in the excel file are: type of macrohabitat (i.e. muddy sand, rubble, rock, live coral, dead framework, live & dead framework), depth (m), slope, ruggedness, broad-scale bathymetric position index, fine-scale bathymetric position index, average current speed (m/s), maximum current speed (m/s), northness, eastness, winter North Atlantic Oscillation Index (same year), winter North Atlantic Oscillation Index (previous year), annual average bottom temperature (same year), annual average bottom salinity (same year). Extraction of bathymetric (depth) and topographic data [slope, aspect, northness, eastness, ruggedness, standardised broad-scale bathymetric position index (BPI; with an inner radius of 1 cell and an outer radius of 5 cells), fine-scale BPI (with an inner radius of 1 cell and an outer radius of 3 cells)] was based on multibeam echosounder data, using the Spatial Analyst and Benthic Terrain Modeler toolboxes in ArcGIS v.10.6.1 Average and maximum current speed values (m/s) were extracted by the ArcGIS v. 10.6.1 Spatial Analyst toolbox using data generated by a high-resolution 3D ocean model created for the MRC by Moreno-Navas et al. (2014). Data for the winter NAOI (DJFM) (Hurrell et al., 2003) were downloaded from the National Center for Atmospheric Research/University Corporation for Atmospheric Research website (climatedataguide.ucar.edu; data accessed on 28/02/2019).