This study presents an assessment of the diversity and spatial distribution of benthic macrofauna communities along the Moulay Bousselham lagoon and discusses the environmental factors contributing to observed patterns. In the autumn of 2018, 68 stations were sampled with three replicates per station in subtidal and intertidal areas. Environmental conditions showed that the range of water temperature was from 25.0 °C to 12.3 °C, the salinity varied between 38.7 and 3.7, while the average of pH values fluctuated between 7.3 and 8.0. In vegetated habitats, biomass values of the seagrass Zostera noltei Hornemann ranged between 31.7 gDW/m² and 170.2 gDW/m² while the biomass of the seagrass Ruppia cirrhosa (Petagna) Grande between 54.2 gDW/m² and 84.7 gDW/m². Sediment analyses showed that the lagoon is mainly composed of sandy and silty sediments. We recorded 37,165 individuals of macrofauna distributed in 63 taxa belonging to 50 families, with a mean abundance value of 4582.8 ind/m² and biomass average of 22.2 g/m². Distance-based linear modeling analysis (DISTLM) identified sediment characteristics, water parameters and habitat type (biomass of Z. noltei) as the major environmental drivers influencing macrozoobenthos patterns. Our results clearly revealed that the hydrographic regime (marine and terrestrial freshwater), sediment distribution and characteristics and the type of habitat (vegetated vs. unvegetated substrate) are the key factors determining the species composition and patterns of macrozoobenthos assemblages.