The dataset provides a quantitative list of the benthic macrofauna taxa, identified to species level, which was collected from soft sediments in the Prof. Luiz Saldanha Marine Park (Arrábida, SW Portugal) between 2007 and 2009, at depths ranging from 10 to 100 m, aiming at describing community structure and distribution as well as classifying and mapping benthic habitats according to the EUNIS system.