Benthic macroinvertebrate assemblages and environmental conditions were studied in Dakhla Bay (Morocco) to (1) characterize the macroinvertebrate composition and spatial distribution, (2) provide a species inventory, and (3) to assess the key environmental variables driving the observed patterns. We identified 9,288 individuals from 67 species. The most dominant taxa were molluscs, polychaetes and crustaceans. The most abundant species were (in this order) Peringia ulvae, Bittium reticulatum, Ophelia rathkei, Mesalia mesal and Maldane sarsi, while the most frequent were (in this order) M. sarsi, Ampelisca sp., Cyathura carinata, Naineris laevigata and Chondrochelia savignyi. The spatial distribution pattern was mainly driven by sediment grain-size and Chlorophyll-a, with hydrodynamics playing also a key role. This gives rise to a structure characterized by three different station clusters, well identified in the Hierarchical Ascending Classification analysis based on abundances, which correspond to a large moderately disturbed assemblage in the centre of the bay, a more disturbed assemblage in the extremes and a transition assemblage in between.