The Oualidia lagoon on the Atlantic coast of Morocco provides important ecosystem services such as aquaculture, fisheries, tourism and high ecological and biological productivity. This is the first study to describe the spatio-temporal distribution of the crustacean community and potential controlling factors in the coastal waters of the Oualidia lagoon. Crustaceans were sampled with a Van Veen grab during two surveys in winter and summer 2013, and taxonomic composition and diversity were determined at 43 sampling sites. Of the eighteen crustacean taxa recorded, fifteen were new to Oualidia Lagoon. Sphaeroma serratum was the most abundant species in both seasons. Organic matter and chlorophyll a content were higher, temperature and salinity were lower in winter than in summer. The structure of the crustacean assemblages was characterised by the formation of two main clusters, organised according to a downstream gradient. Canonical Correspondence Analysis (CCA) showed that granulometry, organic matter and salinity strongly influenced the distribution pattern of crustaceans in the lagoon.