The polychaete assemblages inhabiting the coastal waters of the Oualidia lagoon were studied during winter 2013 and summer 2013. Taxonomic composition and diversity were determined at 43 sample sites. Among the 13 species of polychaetes recorded, 10 were newly reported for Oualidia lagoon. Hediste diversicolor and Capitella sp. were the most abundant taxa in both seasons. Temperature and salinity were higher, and chl-a and OM were lower, in summer than in winter. The structure of the polychaete assemblages was characterized by forming three main clusters, either based on sampling stations or on polychaete species. These clusters were organized according to a downstream gradient, with the stations having fine sediments and a H. diversicolor assemblage in the inner lagoon being replaced by stations with medium grain-sized sediment and a Capitella sp. assemblage in the mid-lagoon, which were in turn replaced by stations having sandy sediments and assemblages dominated by Glycera alba (winter) and P. africana (summer) in the areas closer to the lagoon inlets. The shift was, in fact, from a classical, brackish, lacunar assemblage to two different, temporal aspects of a marine assemblage (close to the inlets), with a transition assemblage in between. This corresponded with a typically paralic spatial structure whose main descriptors responded to a confinement gradient. Despite the absence of a river, the organization of the polychaete assemblages closely resembled that of an estuarine system, with the tidal regime playing a major driving role.