The polychaete assemblages at Dakhla Bay (Atlantic coast of South Morocco) were studied during spring 2013 and winter 2014 to analyze the spatial-temporal variability in diversity and community structure, as well as their relationships with the main environmental variables. Forty-two stations were sampled all over the bay, yielding a total of 22 species (21 in spring, 22 in winter) belonging to 16 families. The three most abundant species were Maldane sarsi (25.1%) Eunice vittata (11.1%), and Nainereis laevigata (10%) in spring and Ophelia rathkei (43%), M. sarsi (21.5%), and N. laevigata (5.9%) in winter. The main drivers of the polychaete community structure at Dakhla Bay were the hydrographic characteristics of the bay as well as the type sediment (in spring and winter) and food availability, organic matter, and chl-a content (in spring). Accordingly, the cluster analysis identified three assemblages in spring and winter, named according to the dominant species. The M. sarsi assemblage occurred in inner bay fine sediments and was replaced by the E. vittata (spring) and N. laevigata (winter) assemblages in mid-bay medium grain-sized sediments, and by the C. tentaculata one in sandy sediments closer to the outer inlet. This represents a shift from a typical brackish, lacunar assemblage to two different, temporal aspects of a marine assemblage, with a transitional one in between. Our study confirms the singularity of the macrofaunal pool at Dakhla Bay and provides a fundamental baseline for future monitoring of an endangered southern Moroccan wetland that will contribute to facilitate its management and protection.