The influence of seagrass on benthic macroinvertebrates was investigated in four semi-enclosed coastal systems in Morocco. Biological and environmental variables were examined in vegetated and bare habitats at four selected sites in two seasons (winter and summer). A total of 28,687 individuals were reported as belonging to 69 taxa. Species richness increased significantly with latitudinal gradient. Macrofaunal biomass varied significantly across sites and had a significant positive relationship with the presence of seagrass in both summer and winter. The DIMO model indicated that the variations in macrobenthic faunal structure were mainly due to the existence of the Zostera noltei; PERMANOVA analysis detected that faunal assemblages shifted within the site and that their variation was enhanced with latitude, in both seasons. A seasonal cause for the spread of macrofauna at all the study sites may be the type of habitat. Distance-based linear models (DistLM) revealed that sediment characteristics (carbon and calcium carbonate concentrations and clay percentage) are the main predictor variables that explain the composition of the macrobenthic faunal assemblage. This study proposes a general model for evaluating spatial distribution patterns at various levels within seagrass-dominated coastal lagoons.